Yes and no.
You can create lists using filters, where MAMEWAH has the info available (basically the stuff displayed using the default layout). So that means you should be OK for the most part, other than cocktail mode (I think someone else may have made a list of these), and no. buttons.
Select a custom list, go into Games List Options > Generate Custom Lists using Filters and you should work it out from there...
I personally do something very similar, and filter using input type etc. for my swappable control panels.
As for horizontal / vertical orientation, as long as you can rotate your desktop (ie using software or hardware rotation), then you can make a vertical layout (eg at 480x640). You can use list-specific layouts, so when you switch lists, the screen rotates accordingly...