Re: making rabbets with router
There is no reason that you have to use a router bit any wider than 3/8" to make hive bodies. The frame rest area is 5/8" x 3/8", so orient the board vertically and use a 3/8" (or 1/2") bit. Since you are using a table mounted router, add a taller auxiliary fence to the existing vertical fence and keep your workpieces pressed against the vertical fence as you slide them past the cutter.
If you are making the rabbets for the corner joints, you can use the same technique with the same bit.
Multiple passes may be a good idea for cuts of this depth, but that applies regardless of the size of bit you may be using.
USDA Zone 7A Elevation 1400 ft