Yes, either that or just pyffi the meshes yourself. See, even if they were pyffied before - regardless whether with an older or with the newest version of Pyffi - the meshes will take no harm if you re-pyffi them.
Yep. Case in point, the current Mart's Monster Mod BSA was PyFFI'd when first posted, but the current version of PyFFI is able to optimize those files another 5% or more.