1. I notice that the normal size of tiles in game is somewhere near 9x9, but the custom tilesets I've seen are usually 16x16, is there a reason for this apart from having more workspace?
It's simply that a 9x9 tileset is difficult to see on a large monitor with normal eyesight. If you like 9x9, feel free to stick with it. Personally I use 20x20 so that the default screen width fills my 1600x1200 monitor.
2. If it is actually possible to have 9x9 tiles for specific creatures, would that stop my screen from stretching farther than I can see it like it does with the 16x16 mods? Or can I have it a bit larger, like 12x12 comfortably?
I'm not exactly sure what you mean here - can you try explaining this again?
3. I have not made tilesets before, but the help files lead me to believe that individual creatures that share the same in-game ASCII symbol can have different tiles set out for them. Am I correct or did I mis-read it?
Yup, that's correct. Unfortunately, this is only true for creatures right now, but that's already a lot of customization (both civilizations like dwarves (which can have custom tiles for each profession, so that a speardwarf looks different from a fisherdwarf) and creatures like dogs)
You'll find the forum is fairly evenly divided between people who prefer as nicely illustrated tiles as possible and those who prefer very simple tiles that remain similar to the original ascii. Both have valid reasons - the fully illustrated tiles look much nicer, of course, but simple tiles can more quickly and easily be recognized.
Have fun!