There are some hard drives that either have trouble fitting or may have some issues with HDL, but for the most part you really shouldn't worry. You said you've had the PS2 for about a year now, so maybe it wouldn't hurt to clean the laser a bit; might improve your boot rate.
"Nagi, how do you feel about being 'normal'? Normal means that if you leave something alone, it just remains that way forever. So if you can't stand that, then you have to be "not normal" in some area... - Seiichi Kirima's dying words