Has anyone ever made a clear carbon rudder for a Merlin? Is it class legal?

Yes it is legal. No restrictions on rudders in the Rules ... aside from horizontal lifting surfaces (or whatever the no hydrofoil rule ended up as).

Clear finish, i.e. black, is difficult to see weed against.

Andy Dalby has a black carbon rudder for the General and has an orange trailing edge to it so he can see the weed still. Looked good, but not sure if he still uses it.

Yup - it's very much alive and works well for weed spotting.