Just finished my deck and installed the Trex Rainescape waterproof system. Planning on wiring it up and finishing it with come cedar ceiling planks. Since this setup is waterproof, do I need to use any conduit for the wiring or will the wet-rated wire through the joists be sufficient to meet code?
If this is outside in any fashion, it's considered a wet zone, even if the area is totally dry. A deck with Trex is no different from a standard wood deck in that regard.
Generally speaking, conduit is seldom not a good idea for any exposed cables. You can then dispense with the UF cables and run THHN/THWN in the conduit (saves some money to offset the conduit). The other benefit is you can directly connect the conduit to your exterior metal boxes.
UF cable can work, but it's not as well protected. The risk is it gets damaged and you have to replace a whole run.
Wire is not allowed without conduit. All exterior conduit is defined as wet. All wire in exterior conduit must be wet-rated. It usually is wet, from condensate if nothing else. A "waterproof deck" would make no difference at all to that.
Wet-rated cables are allowed without conduit, whether or not there's a "waterproof system" above them.