SCC2 (Standard Camouflage Colour 2) is a brown. Mike Starmer's model paint matches are at www.mafva.net
and he is something of an authority on the subject.
Loading would take place inside a naval base so if a truck with a canvas-covered body arrived there it would be ignored by anyone outside (or at least not afforded special interest, as it could be carrying sacks of potatoes, sandbags or any kind of stores) and nobody outside the base would be around to observe the dock loading anyway, so no reason for the truck to be unmarked. In wartime pretty well everything is secret but there are lots of military vehicles around so the locals tend to get used to them as one looks much like another.
Submarines do seem to have been the usual transport but motor launches would also be an option. MTBs were somewhat specialised in their role (and needed for torpedo attacks) so rather less likely, I'd say.