I think the LBS gave you good advice. I think unless you are riding at a competitive level, the advantages of a road specific shoe/pedal system over an MTB one are very small and easily outweighed by the versatility of an MTB shoe.

Also, there is a very wide variety of MTB shoes, ranging from what are basically hiking sneakers with cleats to very stiff and lightweight racing shoes that give up little to road shoes on the bike.

As far as what to get, it's clearly going to be a lot of personal preference. I hate SPD pedals. I find Speedplay Frogs much easier to get in and out of and I like the free float a lot. However, the fact that they have never really caught on after 20 years indicates that they are clearly not for everybody.

I also tried Crank Brothers and Time Attack pedals years ago (not sure if they still even make them). While I much prefer the Frogs, I would've taken either one of these over SPDs.

However, SPD is ubiquitous, and very affordable.