I've replaced a few of the 40-50hp horizontal drive shafts and they've been fine when reassembled using the same shims on reassembly. In fact, the newer ones (04-06) didn't even use any shims. Have been lucky regarding vertical shafts. Haven't had to do one of those (yet).
That said, I haven't had a new style lower unit, like those used on the fuel injected engines (D models), opened up yet. Looks to be a similar design to the 75-90hp motors, so i imagine I'll probably just dive in when I get to one of those. Learning the hard way is my usual way of doing things though....