I'm yet to have any problems with my CTA. 5 months and the filter's still clean! I wouldn't worry too much about agua in the engine unless you're flying through puddles (gotta keep the rocker panels clean).

Ride: 2000 T-red SE
Beats: Kenwood 316S, Alpine MRF200, Orion XTR 6.2, Coustic 400SE
Mods: CTA, Magnaflow exhaust, SVT Instrument cluster, Knuaberized doors, side markers, F***ed up painted headlights.