It may be too late for the OP, but here are some thoughts...

iPods (and all products from Apple for that matter) do not vary much in price in general. Going fron country to country prices do vary a little, due to currency differences, but if there's a concern about getting searched through Customs, a suitcase full of iPods would definitely raise suspicion. This could make the buying trip more of a hassle than anything else.

If you purchase from the Apple Online Store, you can get them engraved for free. This works out great for gifts. Currently customers in the US and Japan can get them gift wrapped as well.

Alternatively, you may be able to find last generation's models through a closeout web store or through the Apple Store's Special Deals section.

Getting them loaded with music (whatever the price of the CDs) would be rather tedious, I would think. Plus, as soon as the employees want to plug them into their own computers to sync with their music libraries there, iTunes will require whatever music you loaded to be wiped off first. iPods can only sync with one music library at a time. There are workarounds to this, but officially this is the way it works.

iPod speakers in your store sounds like a great idea. I can understand why employees would be for this, since iPods can offer a wider variety of music than the typical CD player that might be in a store. I've been there, and 12 years later, I still can't listed to Esquivel, becuase it was played so frequently at the retail store where I worked. If you do have a stereo system already in your stores, take advantage of this and just get a headphone jack to RCA jack dongle to enable the iPod to be plugged into your stereo. If not, then get speakers in which you can dock the iPod. You'll want to select something that is not directional. Many are designed to project the sound to a limited area, and this wouldn't work well in a store. Check out reviews on iLounge.com to see what would work best for your environment. I wouldn't get anything too expensive, since it could get banged around in there or even stolen, and sound quality won't be all that important. Just find something that's a decent value, pumps out enough sound and is sturdy enough to hold up decently. One last note: Make sure whatever music your employees play on it is G rated and universally appealing. You don't want to run off customers with Japanese industrial punk happy hardcore or something.

That's a very nice gift to offer to your employees! They're lucky to have a boss like you.