1. What's the best Ammunition for the Matter Cannon?
Either gold or lead nuggets, from what I've heard. Other nuggets and Matter Balls work too, but are less effective.
Is there a way to get a desert nova / other AM2 flower farm set up? I have tried bonemeal, went through about 8 stacks of it and still haven't seen a single desert nova. Even went so far as to plant grass in a desert.
Magic Bees might spawn them, maybe, but I don't really know. I'm fairly sure they can spawn Thaumcraft flowers, but I don't know about Ars Magica.
Oh, the Aums should pop up spontaneously around Witchwood trees, but I don't think the orchids or novas are renewable.
Does the lamp of fertility work on villagers?
If you're referring to the Thaumcraft lamp that consumes Herba to make plants grow faster, I highly doubt it. The Fertility Serum from Xeno's Reliquary or MFR's Breeder might, though, but I'd still be surprised.
In any case, you can certainly go Vanilla and spam wooden doors everywhere.