Nothing wrong with smaller wheels.

Toe overlap is an issue those of use who are height-challenged just have to deal with. I personally would much rather have a bit of toe overlap than have to resort to using two different wheelsizes with a front one that's a hard-to-find size ala some Terrys. But 26" wheels are common in the US and you should have no trouble finding tubes and tires at your LBS.

Compared to the CrossCheck, the LHT is going to have a 1. longer wheelbase; 2. slacker head tube angle. So, it's probably going to feel a bit more sluggish than the CrossCheck; or, the CrossCheck is going to feel a bit more snappy than the LHT.

Neither ride is necessarily better than the other; it just depends on what you like.

As far as taking up the guy's time--don't worry about it. The shop will want to take the time to ensure you're a happy customer, and getting everything just right on your bike will take a bit of time.