Suicune isn't roaming, he's an event Pokemon now in Tin Tower. This isn't something I added, though, just a change in Crystal from Gold/Silver. As far as Raikou and Entei, they both show up in my Pokedex, as well as change their locations, so I'm not sure what that issue could be.
EDIT: Doing some research, there's a bug called the Roaming Roar bug in later Pokemon games, where if a roaming Pokemon uses Roar and escapes, it disappears. It's not in Crystal, but me messing with the code could maybe have caused it to happen... although that seems extremely, extremely unlikely.
My next suggestion would be perhaps what I should have mentioned first, given the basis... the question is: have you encountered them in the wild yet? They won't show up just based on your encounter with them underneath the Burnt Tower, you need to find them in the grass first for them to be trackable. For some reason, I seem to ALWAYS initially find them just south of Blackthorn, fwiw.