Oh, I'm with you on that one, pet-hate-wise... Especially when the 'tray charge' is in really, really small print at the bottom of the menu. And they can be quite absurd (step forward, Chedi Milan, with its 12.50 euro charge, advertised in 8-point-font... unsurprisingly, that hotel didn't last).
Unfortunately, I'm pretty sure that the 'tray charge' doesn't go to the waiter, in most hotels. When it's a 'service charge' (of 18%, or whatever), I do tend to regard that as a tip - but as the hotels will often just pocket the 'tray charge', I'll try to give the guy another couple euros in cash... I agree it's ambiguous, though - seemingly a way for the hotel to put one over on the guest and the waiter at once...