To answer in reverse order....
The volume displacement method is an excellent way of measuring the change in the aluminum can size before and after testing. That is much better than your original idea of measuring the can dimensions with a caliper. You will also want to measure the can this way before freezing the water inside, so you can know what the change was.
I don't think that poking a hole in the can and filling it, then sealing it, is very different from using a pop-top can, filling it, and pulling up the tab somehow and doing your best to seal that.
Either way, the sealant may prove a weak spot and burst, leaving you with the same result as just pulling up the tab as best you can but leaving it open a little bit. Sealing the can has some advantages with respect to not spilling any water and ensuring the same amount of water is freezing in all tests.
My instinct would be to not introduce a weakness into the can along the side or bottom. (if you must punch more holes than the tab, to it on the top). Soda cans are designed to be under pressure and their geometry tends to encourage the "fizz" to escape out the top rather than have the can explode. You'd change that if you poke a hole in the main body.
I'm not actually sure how likely it is that the can will rupture if you freeze the water inside. My recommendation would be to do a couple tests of your process. First fill a can with the tab open, freeze it, see what happens. Then try another one with the tab pulled up and sealed. In both cases you probably need to be careful of the other contents of the freezer in case the can bursts or the contents push out of the top during the process. Put the can in a tupperware or similar plastic bowl, to capture any liquid etc that might escape.
You may find that the easiest approach is to not fill the can all the way, but to mark the level at which you filled it, then do the volume test to that measure on the can. When the water freezes, immerse the can+ice. This requires a bit of correction for the parts of the can not filled when you begin, the volume of the aluminum. You can correct for that by getting a volume measure of the empty can, and subtracting the amount of water added to fill it up to the line.
So that's a lot of ideas tossed out with the main thought being "try it both ways and see for yourself". (This can be a useful experimental approach if it isn't too expensive in the real world. This is however an "engineering" trick rather than "science". Building lab apparatus to do experiments though often tends to need some "cut and try" to make do with the materials you have and still test your hypothesis)
Whatever you decide, the first time you do it, as a safety thing, you need to protect the contents of the freezer from your potentially explosive can. There are a lot of possible failure modes for a sealed aluminum can (it might rupture along the side, the top might be pushed off, it might burst along your sealing or it might just deform like you are expecting. It's also possible the can may prove so sturdy that you can't measure any volume change, but that is probably unlikely). If it gives way while there is liquid in the can, the can might spill all over the freezer, then turn to ice.
The easy way is to stick the can in a bowl big enough to hold the can and its contents, and stick the bowl+can into the freezer.