I have a 1994 90HP Yamaha on a 17' Key West.
Recently, this started happening: sometimes when I lower the motor, it makes a slight but distinct crunching noise. As far as I can tell, the noise only happens when the trim pistons are engaged (as opposed to just the tilt piston). The crunching sounds like the crunching of hollow seashells under your foot. There is nothing visibly unusual with the power trim unit, and I don't see any obstructing debris.
I live on a canal with a lot of weeds. I troll out with the prop tilted up high (almost breaking the surface). Once I'm on the lake and ready to gas it, I lower the motor. That's usually when I hear the crunching noise.
More consistent, however, than the crunching noise is a "waviness" to the power trim. Before all this started happening, the power trim made its very consistent high pitch whir as the motor would be lowered. Now, once the power trim pistons are engaged, that "whir" wavers slightly in pitch and volume.