I don't know if Atari followed any industry standard for their key designs. Also, I've never encountered a buckling spring ST keyboard; original ST keyboards used collapsing rubber dome switch contacts (domes from ebay, no affiliation). For the upper portion, your best bet is to copy one of the other keys in the same row. You should be able to pop the caps off pretty easily with a flat-head screwdriver. FWIW, all of the Atari keycaps I've seen (520 STFM, 1040STF, 1040STE) use the same design; not sure about the detached TT keyboard but going by feel, the non-function keys also appear to be the same design (the TT function keys feel totally different though).
As far a creating a 3-D model, I'm not aware of any existing ones. However, the external Atari key designs are much blockier than what you'd typically find on e.g. an IBM keyboard so should be much easier to model (no complex curves). The Delete key on ST and TT keyboards is in the main block of keys (to the right of Return, below Backspace) and not on the numeric keypad. The key labeled '. Del' on PC keyboards is just labeled '.' on the ST/TT.
AFAIR, the specfic key you're missing has a unique shape so you wouldn't be able to directly copy one of the other keys on that keyboard. Honestly, your best bet might be to purchase a replacement key.
Image source: Wikipedia (Bill Bertram, CC-BY-2.5)