I don't think a great deal of attention has ever been paid to grain orientation in ebony on vintage fingerboards. Ever. Much of the time, even looking at end grain will tell you little or nothing. It's not typically revealed by cracks from aging, but it does become somewhat evident during refrets.
It's not hard to tell if new ebony is quartered. You do it the usual way, looking at end grain, or for medullary rays on the radial surface. It's hard to tell when looking at an 80 year old guitar, though.
That's the trouble, it really is hard to see, especially on old ebony, which is what you asked about. It's not hard to discern when you're in the process of a refret, however. Often you can tell by the behavior of the wood as the old frets get pulled, and also when you plane the board to true the surface. I've been doing this for over 40 years and that experience informs my take on whether any attention was paid to verticality of grain.
I'm still not certain what you hope to gain by this inquiry. I will make one comment though, that you might be able to use: the ebony used on vintage Martins was mostly (if not entirely) from central Africa. Most of the ebony you're likely to find today comes from south India and SE Asia. Some of the African "ebony" was actually Dalbergia, not Diospyros. And pretty much Africa is logged out, and has been for some time. The African ebony I see still available is Diospyros. I think you're never likely to be able to tell the difference in African ebonies unless you can ID the exact tree it came from, or choose to rely on anecdote and folklore. Asian ebony tends to be streaky and grayish or brownish. Many dye it full black. It's still quite nice, dyed or natural. I also think the Asian stuff is harder and more durable.
My inquiry was motivated by a coupIe underlying questions: 1) does it make a difference in sound, stiffness, or stability if the ebony fretboard is quartersawn vice flatsawn? 2) If I wanted to reproduce a pre-war Martin design as closely as possible, would I need to use quartersawn material?
I'd say no to both, though you might want to scout out some old African ebony. It's still allegedly available. Gabon (sometimes called gaboon—rhymes with baboon!) is one trade name. I can't vouch for the authenticity of what's on the market now, e.g.: http://www.cookwoods.com/Weekly Specials.htm This stuff seems a little scroungy to me, but I'm only looking at photos and reading their description. I just got this in the email yesterday.
Gabon itself (the country) is pretty devastated, but that same timber grows across DRC, and there are probably old stashes here and there in the US and outside Africa. You know it because it's lighter in weight, has more obvious pores, and is usually dead black, without dyeing. It's really different stuff than the Asian ebony. I personally don't believe that's a make-or-break difference considering all the other factors that combine to make a guitar, many of which are far more important, but if you want to cross the I's and dot the T's, you might want to seek out that flavor of ebony.
Where da heck is Frank? He should have something intelligent to say on this matter.