I deleted an individual sim or two a few years ago and will not do it again. I had problems with stuck sims, sims dropped partially down into the floor, and invisible sims. My advice is not to do it, per my experience. I did it in 2 but will not in 3. I evict sims and let them die on the clipboard all the time with no issues.
Did you have the stuck/partially in the floor/invisible Sims in TS2 or TS3?
As another poster pointed out, they're more interconnected in TS2. In TS3 the memory system is a bit different (and crappy IMO so I shut it off).