I'd build the cubbies oversize and just put bookshelf speakers in them. Overnight Sensations would probably be a good choice, although I have no experience with them. Speakers sometimes sound weird if boxed in. Might want to surround them with fiberglass or something with a full grill covering the cubby. Maybe the back of the cubby also open with grill cloth there too.
Just tossing out ideas here and speaking out my @$$.