I think a lot of people assume reliability to be an engine that runs good for a long time without any maintenance. There is a fine line betwen reliable and the amount of hours you can put on a stock/modded engine before you can expect it to fail, or have the performance start to drop off.
So, you have a stock SJ...it runs good and strong for a good 2 years until you decide you want more power. You take it down to your local builder and get a re-bore, throw a pipe, head, reeds, prop etc on it. Suddenly, after only one season on your new powerful boat, something goes wrong, and instantly, you look for someone to blame.
Stock engines are made to take a lot of punsihment AT LEAST until the warranty period expires. Any mods to said engine will make it wear faster and therefore see you replacing things more often. I know of a 61x cylinder with porting so severe (read: absoulutly screamed!) that it would need the pistons replacing every 6 or so hours because the porting mechanically trashed the pistons so fast. The point? Replacing pistons so often os a trade-off for having something that was a good 3mph faster than the other ski's on the track.