Why would you want through threads t nuts (unless you are using them for an entirely different purpose)?
First off, let me say that I agree with
@Dabbler 100%. Staked or part threaded nuts are the safe and smart way to go.
But they are not complete protection from this issue.
Personally, I almost always prefer to use socket head cap screws carefully selected for each application over those horrible threaded studs you get in the kit.
The main reason I prefer them is not because I like the way they look (although they do look way better than a threaded stud). I like them because they have high quality threads that are very consistent with easily controlled torque characteristics.
I don't worry about bottoming out the screw because each application is carefully selected to make that impossible. But even more importantly, I never apply more torque than the cast iron can handle - regardless of whether or not the screw bottoms out.
Some history is appropriate here.
I got my first clamp set 50 plus years ago when I was using my drill press as a mill. It has thrust bearings and a chuck with a threaded retaining collar. It was basically a horrible milling machine but it was still infinitely better than nothing. The table is slotted and has an x pattern of drilled holes in the traditional way of drill press tables. There are no bottoms in the T-slots that a through bolt could bear against. I also bought an x-y table for it which had T-slots with bottoms.
When I mounted the x-y table to the drill press table, I discovered that some idiot had not tapped the T-nuts all the way through so I couldn't torque down the Bolts. So I bought a tap and finished the job properly. As a 20 year old I had no idea that there was a reason for the way those nuts were partially threaded like that and there was no internet yet to learn anything from.
That old drill press met my modest milling and drilling needs for forty years.
Perhaps by luck the much bigger Mill/Drill I got 40 years later (10 years ago) used the same size T-nuts so I used them and at some point I encountered the bolt bottom issue. To me it was just a simple artifact of a nut sliding in a cast iron T-slot. Not a lot different from a shallow drilled hole. I simply installed the bolt to the right depth first and then slid it into the slot to where I needed it. In so doing, the bolt also makes a handy handle to move the nut with. Occasionally I had to remove a bolt in situ. In particular, I had a few tools that had base mounting holes instead of flanges. In these cases, I would simply thread it in all the way by hand and then back it off. Life was good for 10 more years.
In the search for a better milling machine I bought two Bridgeport sized Knee Mills last year. But I had used up all my T-nuts at that point and needed a few more. So I ordered some from KBC. That's where and when I noticed that you could get them threaded through or partially threaded and my head was instantly filled with the big question WHY would anyone want partially threaded?
It's the exact opposite question from what you asked!
The magic of the internet answered that question fast. But with 50 years of experience using threaded through nuts behind me I ordered threaded through anyway. It's what I was used to. But by then I also had much more knowledge of the issues. Let me explain why.
Throughout my career I have more or less constantly had to deal with fasteners and their issues. Fasteners are so important to an automotive company that we had an entire department of fastener experts whose job it was to monitor the work of the various design groups, provide advice and information, do detailed analysis, develop new fastener technology, and approve fastener applications in vehicles. I learned a lot from them over the years. There is a lot more science that goes into a threaded connection than most of us realize.
While I totally agree with
@Dabbler's advice for anyone using T-nuts, I would add a few other pieces of advice all aimed at the exact same problem arrived at by a different path.
That T-slot in our mill tables is a vulnerable piece of hardware. You can break a piece off exactly as we have been discussing. But you can also break a piece out using a bridge clamp exactly the same way whether or not the nut is through threaded. You can also break it using a simple ear clamp or a bar clamp or for that matter ANY application where the part and table are not in contact with each other in a compressed column. Cast iron can easily handle a high compressed load. It cannot handle a high bending or tension load. The stress/strain relationship for cast iron is not a curve that bends. It is a line that ends .... at fracture.
Depending on the type of cast iron or steel, cast iron's yield strength is about half that of regular steel. In general, roughly 30,000 psi for regular cast iron vs 60,000 psi for regular steel or 130,000 for a grade 8 bolt.
Unless there is a pinched (compressed column) stack of metal between the top of the table and the bottom of the bolt head or nut, a tightened T-Nut bolt exerts the same kind of load on the T-slot as a through bolt that reaches the bottom of the slot. In other words, the half threaded nut protects you from a bolt run too deep, but it does nothing to protect you from a non-compressed joint.
A stacked compressed joint does not try to rip apart the top of the T-slot - instead it squeezes everything together. But a bridge connection, or a side clamp, or an ear clamp does. The worst of them is the bridge clamp. That's those long slotted forged bars that come in the clamping kit. They look like this:
The longer the bridge between compressed columns, the worse the problem.
To deal with this, I developed my own standard rule of thumb for using T-slot Fasteners. Never torque the fastener beyond the strength of the cast iron ear of the T-slot. The torque I use is just 10 ft pounds (120in-lb) on a lubricated 1/2-13 machine screw. I can also use a short Allen wrench tightened by hand but not gronked. 10 ft lbs generates 1500 pounds of clamping force and about 10,000 psi of stress in both the bolt and the cast iron T-slot. Although the T-slot has a, bigger cross sectional area, it is significantly reduced by the slot itself. The stress numbers I chose are conservative. I suppose I could use a higher number but I don't like to push things. I don't have access to any fastener experts anymore and I don't have a CAE Workstation to model the stress in the cast iron T-slot Ears. 10,000 sounds safe to me and 1500 pounds of clamping force per fastener seems like more than enough too.
So there you have it. That's really the reason that I don't worry about threaded through nuts myself.
For reference, these are my vise Clamps. They are oiled and tightened to 10 foot pounds each. Notice the nose in the vise groove. What you can't see in the photo is the foot opposite the nose and the gap between the clamp and the table under the screw. No unthreaded section in the T-Nut would stop that table from cracking if I overtightened that screw.
My advice to others is: 1. Use an unthreaded or crimped T-slot nut. 2. Regardless of the type of T-nut you use, never tighten the nut or bolt beyond 10 ft pounds unless you know exactly what you are doing. 3. Avoid high torque with bridged or nose end Clamps or any other uncompressed column.