Absolutely. The E-magazines are generally newer and therefore likely to be in better condition than most A12.
For some reason, the E12 seem cheaper on the used market than the (newer-style with slide holder) A12N... Not sure whether this also applies to the E16.
I personally use a couple E12 I got for a good price. Never had an issue.
EDIT: just had a look at E16 and A16 prices on that famous auction site... price seem through the roof. Crazy. I think that shooting regular 6x6 and cutting away 1/3 of the roll whenever 645 format is desired definitely costs less.