In Yamato III the dimensional subs had to "surface" to warp (making them visable when they left warp before they could "submerge" again.)
One thing of note that might have been missed, the submarine was using propellers for thrust in dimentional space rather than its regular engines. This would suggest they have their wave motion engine on battery or something. In theory that means they can't stay down there forever. A newer model might improve on that though, as it is suggested this might be a one of a kind ship presently in the Gamilas Empire.