I use butt joints, 100% waterproof glue and screws. Using screws saves tying-up cramps. I prefer to paint 'em both inside and out - with whatever colour happens to be on the brush. Edges waxed to stop sticking.
I used to make boxes using pallet wood - which is mostly pine - but I've just finished a batch of nuc boxes which started-off as Mann-Lake glued cedar brood boxes, which were then cut in half:
New sides were then added using Oregon Pine Studding recovered from pallets, with glued and screwed butt joints, and grooves cut into the inner sides for feeder-dividers so that they can be used either as 5-frame nucs or as dual half-size-frame mating nucs.
Polyester filler was applied, sanded down and the boxes finally painted with industrial floor paint.
I'm pleased with the results and will be making a lot more in the same way. Starting-off with commercially-made flat-pack boxes ensures that the boxes are totally square and without any twist. When taking construction time into account, including that for the recovery of timber from pallets, this method is a far more economical route to adopt (for me) than making boxes completely from scratch using reclaimed wood.
But I'll continue to make bases, roofs, feeder shells etc from pallet wood.
LJ