Yes, in Bluestar's Prophecy they are the parents of Bluestar, and her sister, Snowfur.
So they are mates.
But does that really answer the question of weather they loved each other? They showed like zero affection and hardly talked during Bluestar's Prophecy. I might say no.
Goosefeather says that Moonflower makes mistakes, while looking at Stromtail, I think its possible that Moonflower loved Stormtail, but Stormtail thought nothing of their "relationship" and their kits.
Stormtail is busy helping Dappletail while Moonflower is fighting for her life, and even before Moonflower dies it is obvious he loves Dappletail. Most of the clan are surprised Dappletail and Stormtail never haver have kits. I think no.