The only issues of removing the balance shafts (yes, there should be two in the housing) is that it will void your warranty (but they would have to take the pan off to even know), you may not like the vibration (but your girlfriend will), your engine mounts may wear faster (but probably not so much), and you'll have to use more of that expensive oil. If you remove it, I recommend using the oil sump baffle at focussport.com to ensure your oil pickup stays submerged during cornering and stopping/accelerating.
Aftermarket Internals (Pistons, Rods, Crank Shaft)
If you plan on upgrading the internals, removing the balance shafts is a must. Of course you would do this anyway if you are in the block, but dont put it back in. The balance shafts will actually increase vibrations and crank bearing wear if components of weights other than the stock design are used. You would have a better chance of winning the lottery than having the balance shafts phased correctly after changing weights of these components.
If you are using stock internals, which most of you probably are, and are concerned about additional engine wear, know that the balance shafts do nothing to help "primary balance", and only deal with "secondary balance". Therefore, there will be no effect on crank thrash. These three links should tell you everything you need to know about balance and balance shafts. The third is most specific to most of your concerns.