As far as Moogle Mail moogles being visible while accepting the new lore of moogles being generally invisible, I would definitely go with the idea that they can make a conscious decision to reveal themselves to anyone if they want to.

As far as why they are invisible in the forest now and weren't in 1.0, I'm not sure. Maybe while the Calamity spurred some into helping out, it scared others into hiding even more than they did before. Next one could be spoilers so into HB tags it goes:

Also, I recall a quest during beta where Ul'dahn merchants were trying to poach moogles. Perhaps this sort of illicit activity only began recently and that has driven the moogles into greater secrecy.


These are both purely conjecture however: I wouldn't say either has any strong evidence going for it.