I very rarely used nukes in Civ2, unless 1. I had had them used against me, and 2. I was confident that I could take out the city I was nuking with paratroopers (back then nukes cleared out all units and you could paratroop right in and capture the city) and hold it long enough to clean up the pollution. It did make it more realistic than Civ3 in that regard because you just wouldn't hit the button on something that was going to cause you 80 points of pollution damage if left undealt with.
You are right about Manhattan project, Hb. The thing is, though, that other civs might not be advanced enough on the tech tree to actually make the nukes, or they might not have the resources/population/infrastructure to do it quickly.
As someone posted in the other forum, anyone getting the Manhattan Project in Civ2 it was like the horn of the apocalypse blowing. Very scary. You fought tooth and claw to make sure it wouldnt happen or researched your assets off trying to get SDI.