Random thoughts that aren't worth much --
As stated, hypothyroidism can cause hair loss and skin issues. Probably unlikely, though, given that it's occurring in both of them and they're young dogs. It's more an issue with middle aged and older dogs. I assume, as with people, that there's a hereditary connection with hypothyroidism in dogs. But it still would be very odd I think for it to occur in both of them at the same time.
The oily form of seborrhea can cause hair loss and scales, although there will usually be a lot of other symptoms (greasiness, overall itchiness, odor, etc.).
Color dilution alopecia. A genetic condition that can cause hair thinning and flakiness. Doxies are one of the breeds it occurs in. Apparently only in certain colors, though. So may not even apply to your two.
Cushing's disease can cause hair thinning, especially along the sides. Again, I think this is unlikely given their relatively young ages and that it's occurring in both of them at the same time.
Since it's occurring in both of them I'd (obviously) be considering something environmental or genetic. If they're not prone to having sensitive tummies I'd consider a food switch.