Intuitively, I concur with Garry regarding fore = north.
Since port = left and starboard = right, it feels natural to translate that equivalently into a 2D top-down map view, which means fore = topwards/up. And of course, on most of today’s conventional maps, up = north.
So, via that assocation, I’d personally like it best if fore, top, and north were aligned.
I almost tend to think I’d rather learn a new abbreviation for starboard (ST or SB, so it doesn’t coincide with S) than learn to deal with the changed alignment. Since nautical directions are relatively uncommon in IF, it might not even be too bad from a UX perspective to ask players to memorize a different command shortcut. (Admittedly, the issue would remain that someone might mistakenly enter S while intending to go starboard, and would be irritated by the resulting south/aft movement.)
If such a change is not on the table, or in other words, if fore = east (as you said in the OP) is settled, then I think you could decide what should be at the top side of the included map representation by looking at which set of directions you mostly use in your room descriptions, as those will probably influence what the players will orient themselves by, and what they’ll type.
If you mostly (or only) use compass directions in the descriptions, then stick to north = top as usual, and let players who want to use nautical directions deal with the mental translation on their own (the port side of the ship will not be represented on the left (etc.), but so be it).
If you mostly (or only) use nautical directions in the descriptions, then use fore = top, so that there is an easy, natural(?) mental mapping with port = left etc.; the coincidental fact that fore is also east (and therefore north unusually mapped at the left etc.) will only be important to the players who want to use compass directions (but their number might be low because they’ll be deterred by all the nautical directions in the prose).
So whatever has the primary role could determine what’s at the top side of the map.