My AC blower is in the attic. It has a number of low voltage control wires that are not in a junction box. I am planning on blowing insulation into the attic, but I am not sure what to do about the wires. Should they be in a junction box?
It is not required, but it can be a good idea. Personally, I would prefer them to be in conduit (e.g. ENT/smurf tube) with splices in junction boxes. Just like with electrical wires, it will protect them from damage while providing accessibility for splices.
Low-voltage wires are typically thinner and less durable to begin with, so protecting them is a good idea. Conduit may be overkill but it also makes it easier to pull new wires later on if needed: do a search on this site for people running into trouble with incorrect/insufficient thermostat wires for reasons why this is a good idea.
While the NEC does not concern itself with low-voltage wires (mostly, they are mentioned in a couple of places), nobody would fault you for providing the same levels of protection and accessibility for these wires.