How modifications affect your reliability depends on your definition of reliability. If by reliability, you mean the ski starts and runs good, then that's just about keeping things in good working order, cleaning them, etc.
If by reliability you mean long crank and piston life, then every modification you make reduces that definition of reliability. Your filters technically add more power, and reduce engine life, but the amount is so minimal its negligible. You just have to decide what amount of engine life you are willing to trade.
For me, I am willing to accept that my high compression head, pipe, lightened flywheel, etc, increase my peak RPM by 1000rpm and place more force and heat on my pistons, crank, etc. I believe a setup like this is good for several years, a few hundred hours, unlike a stock boat that might run every summer indefinitely.
You must decide how you define reliable.
My advice is look up the IJSBA rules for what mods you can have, and start with stock class. Move on to limited mods when you are ready. I realize you may not be racing, but it still applies.