as others have pointed out, this is actually not true. It is not "recommended" that centers be horizontal for performance reasons, it only happens because that's the only way to get a speaker under/over a TV screen!!
in an ideal world, you'd have identical speakers identically oriented for all channels. The RC-LCR (like pretty much any speaker) actually performs better vertically, but like others have said these "rules" are just recommendations and you do the best you can given your constraints (wife included ).
thankfully LCR type speakers are designed to operate either horizontally or vertically, with wide dispersion in either axis, so it should still sound great with three horizontal RC-LCR's across the front.
all plugging the ports does is cut off the lowest octave or so of bass output, and also reduces the speaker sensitivity slightly since it isn't "reinforced" by the port. But the sound will still be sweet and clean. Instead of reaching down to 50Hz, the RC-LCR will probably get to 80-90Hz with ports plugged, still plenty good enough if you have a subwoofer to fill in the bottom.