I didn't think Mopar made lowering springs for the Commander, are these new springs for another Chrysler vehicle that just happen to fit the spring perches of the Commander? If you haven't already, I would check the Mopar Catalogue and confirm that Mopar Accessories/Performance actually sell these and what they charge for them, before trusting someon on ebay, that these are legit and the best price.
Lowering the vehicle makes it more likely to bottom out and bottoming out will damage the shock/struts. Unless its really bad, it won't damage them right away, but people that lower vehicles often find the strut/shocks wear out many time faster than when stock.
Lowering also moves the range where the shock/strut was designed to operate, that can effect it performance and/or longevity.
The less you lower, the less the effect these have. I would think a Jeep, with a lot of suspension travel already designed into it, would NOT run into some of the common problems on other vehicles, if you kept the lowering to only a small amout.