Depends what sort of wako they were. Several clans were no more than pirates but had the money and resources to have quite substantial fleets. The typical clan ships would be similar to those below.
If the wako were more of a bunch of ragamuffins then any ship they could get hold of would suit but they would still be mainly Japanese in design as they would be able to sail around the coast of Japan without getting set upon or having too many questions asked.
The low, open sided one pictured below would be fairly common and varying designs (usually size) would have been seen.
Picture taken from the internetDon't forget that a lot of the none-clan wako bands would've been formed of Japanese, Chinese, Korean, Malay etc and occasionally Western pirates and the vast majority would have island bases from which to raid from.
If you've got any more specific questions then ask away
cheers
James