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I played my first game at a gaming store, a 3v3 to make it even more intimidating, and came across something that made me scratch my head.

I believe I lost about a third of one of my (IG) Vet teams in the shooting phase, so I get ready to roll morale, and ask them just for confirmation. They told me that Morale tests are only for Assault combat. The mini rule book I have says when you lose 25% or more of a unit in shooting/movement phase is a time to make a test.

This was a 3v3 with people who all looked like they knew each other and have played for a bit. So, I'm wondering...is this likely a 'home rule', a mistake that they've been making since 6th came out, or a rule change that came out after the book?

Either a home rule or mistake. You were 100% correct.

How four other guys could stand there and let that silliness pass is a mystery. They must have been playing a joke on you, as the new guy.

Its quite possible they were giving you a break. Perhaps being your first game they didn't want to dishearten you. We tend to do similar things at our LGS where if a new guy is getting a hard time we let them reroll charge ranges for example. However the rules are the rules, if it was the case that there should have been a morale check they shouldn't say that this isn't the case becasue it would cause confusion but they could have let it slide or given you a reroll. I dunno I suppose is speculation.

I think it's a house rule, as it makes sense.
You won't run in the open from cover when shoot at, even if you panic, you try to dig deeper in cover. In assault you run away.