Sure. The OED even lists them as contemporary coinages:

[1965 Wireless World July 49/2 (advt.) Contact tail variations..include..tails for direct mounting to a ‘mother’ printed circuit board.] 1965 Electronics 6 Sept. 36/1 Nine daughterboards, each carrying 30 circuit packages, go on each side of a motherboard.

However, that's just an analogy: it doesn't actually tell you anything about what the motherboard does or why. In that sense, I think mainboard is actually a bit more descriptive: it's the principal interconnect between all of the device's parts.

Why not just… the “board”? It’s the only board. There are no other boards, as the things they used to call daughterboards are now “cards”. You plug cards into the board. Board goes into case.