Should I complain about employees at Subway closing an hour early?

Absolutely complain. 

Just make sure that the employees that get in trouble don’t know who you are otherwise you might get some extra special sauce on your sandwich next time.

maybe they have a reason , dont stay open for 1 customer who comes late , or you a manager of the store .

absolutely.....mention it to the manager.......maybe there was a good reason, but even if there was, it might be good for a coupon for a free sandwich  since you were put out. 

You can, but that dosen't mean you should.  I've worked fast food - and the days I closed early were the days I didn't need any more grief from anyone.  If it happens on the regular I'd call and talk to the manager in the morning (managers always work the am shift).  Most likely the people working there just had one of those days, I'd give them a break.

I would complain if I drove all the way there just to find out they were closed.

Slow day, close up early. Save money. 

Good luck finding the owner. They don't make themselves known much, apart from a few posterboys they use with advertising to potential new franchisees.

Yes.

If there was a reason for it being closed then they have nothing to worry about.

Don't bother it won't get you nowhere.They will just make up some excuse.