Is it ever explained why the three Dwemer ruins in Dragonborn weren't there during Bloodmoon?

It's called "Map not to scale."

In Daggerfall, it's established that the areas of High Rock and some of Hammerfell amount to about twice the size of Great Britan. Vvardenfell is about the same size, and Solstheim is probably about one-half to one-third the size of Great Britan.

In Morrowind, Solstheim as implemented is nowhere near that. So, it stands to reason that the Dwemer ruins were always there... they just weren't important enough to implement in Bloodmoon.

That makes sense, but for some reason, Solstheim feels smaller then it did in Bloodmoon to me. When I did the quest involving Ft. Frostmoth, I got there much faster then I did in Bloodmoon. The Skaal village also feels smaller and more narrow then it did in Bloodmoon.

Everything in Morrowind is more stretched out with a lot more empty, flat space. Fourth Era Solstheim is much more dense. Also, the endless fog made everything in Morrowind seem larger than it was.

Reason? Kagrumez was buried underground, Nchardak was underwater, Fahbltharz was buried within the mountain.
Actual reason? Diversity! Plus it gave Beth and opportunity to add some really sweet dungeons.

No one ever said Bethesda does the best job when designing their environments.

Red Mountain exploding probably unearthed them.Solstheim would have been hit by earthquakes being that close to Vardenfell.Also take into consideration the massive amount of ash fallout on the island.Most of the barrows that were in BM are sitting under 200 years of ash build up...provided they survived intact from the initial shock wave.