Agreed - shim the discs so that you can swap wheels without any further adjustments. Did this with my Hybrid. The Disc Shims you need are made by Syntace and come in a pack of 8. The shims are 0.2mm each and I've only needed to use one per wheel to date to get the discs centralised. Bought mine from the Australian Distributor's site direct, arrived express post next day. Fantastic service.
http://www.eightyonespices.com.au/#!buy-syntace/c1z0u
Stating the obvious, make sure you source disc specific rims. They're usually stronger than those used on rim brake wheelsets. Choose the inside width based on the tyres you intend running. I'm running 700 x 32c slicks on a 17mm inside width rim, front & rear, and they're okay (Mavic A317 Disc) but not optimum. For comparison, Giant fitted Alex DA22 road rims on their 2010 Seek hybrid models coupled with Maxxis Columbiere 700 x 32c wire bead tyres, and the DA22's only have a 14mm inside width. Trend nowadays is to go for 19mm - 21mm wide rims with tyres 25c - 32c to overcome the 'Lightbulb' effect. My 700 x 32c Schwalbe touring tyres are mounted on 19mm rims (Mavic XM719 Disc) and are noticeably superior in hard cornering. (Not really a fair comparison to the factory fitted cheaper Mavic rims, the Xm719 Disc rims are fully welded & much stiffer) Wider rims encourage hard cornering & reduce tyre wall flex. Note that the two Mavics are considered MTB rims.
Check out the ETRTO designation in the spec for each rim you are considering - in the case of the Mavic A317 rims above, the listed size is ETRTO 622 x 17 and the Mavic XM719 rims are listed as ETRTO 622 x 19 (622 is the sizing standard for 700c & 29er rims) The good thing about any 700c disc braked hybrid is that you can quickly swap wheels around with slicks, touring tyres or even MTB knobblys.
As your usage is road oriented, you will be looking at more specific Road Disc rims, (which tend to have a more Aerodynamic profile) are lighter, and usually don't have eyelets.
Suggest you consider those factory fitted wheels as entry level suitable for training/commuting and look into building a better wheelset for racedays. Any LBS will tell you that wheelsets are where most of the larger manufacturers cut costs on components - Giant along with others are now using their own self-branded hubs on most of their range to make it harder to determine component levels against their competitor's offerings.
Cheers