If the spell list doesn't say you need the material present, I think they can cast the spell regardless. I don't think that's meant to be a universal requirement for all wall spells, otherwise it would appear in 7.1.13 and also be noted on the other spell lists.
Ignoring that for the moment, if the requirement did apply, it seems like a GM judgment call. Hurin's answer is perfectly valid. I think at most the effect on the wood of the boat is informational, and there normally isn't an RR vs informational spells in RMSS, so that gives the same conclusion, unless there are enchantments on the boat specifically against informational/detection type spells.
In my game, most of the wall spells work by shaping existing material, so in that case an RR would be required since the wood is actually being affected. If you change how spells work, though, it's a good idea to let the players know before they are using them.