Yes, you will need to connect all three connectors, as leaving them open will damage the radio's.
IF you just want to connect two antenna elements, you should have a so-called terminator (example: http://www.digikey.com/catalog/en/partgroup/rp-sma/23723) to prevent the radio from being damaged.
And then, yes, with just two antenna elements that RF performance will be reduced to a maximum of 2 spatial streams.
Also make sure that the antennas you install are part of the same antenna system; so you can't install two separate antenna's and point them to different directions as it will result in very strange behavior. The three antenna connection are on the same radio (different radio chains though).
Please contact your partner or local Aruba SE if you seek advice.