Yes, this has happened to mine this year. My 23 yr old mare was the worst, though my 14 yr old gelding coughed a few times too. Had the vet out, and he attributed a few things to it. Mostly, they got some dusty hay (my fault) and developed IAD (inflammatory airway disease).
I think getting blood work is an excellent bit of advice. Will help pin down whats happening.
Let us know what you find out.
Be the kind of woman that when your feet hit the floor each morning the devil says, "Oh crap, she's up!".