That's weird, the smaller LBS's in my area normally stock only the 48 mm stems, the larger ones have all lengths in stock. I've never had them push me toward a longer stem. I agree that 38 mm stems are getting harder to find, but that's only because the shallowest rims are getting harder to find!

I'm guessing that your LBS has had experiences where people have bought tubes with stems that were too short for their rims, then blamed the LBS when they got stuck with a flat tire in the middle of nowhere. If they sell everyone 60 mm stems, then at least everyone will be able to use the tubes they bought.

I've been on a ride with someone who forgot to swap his spare tube out after switching to deep aero rims - and just the other day someone here posted that her DH had stocked her seat pack with the wrong tube.

I'm with you that it's best to use the shortest stem length that will work with your rim and pump head (different pumps grab different lengths of valve stem). Lighter, less angular torque on the valve stem if you aren't completely smooth with the pump. But if someone doesn't know what stem length she needs, I can definitely see the bike shop just selling them 60 mm and being done with it.