Don't the creep colonies kind of not exist anymore?
Anyway, I think they might keep the tumor-like appearance. Just as you don't see a caterpillar sprout wings and become a butterfly, or a hydralisk getting shorter and growing more legs to become a lurker, I don't think you'll see buildings just transforming. I think that the skin that grows over is a bit like an egg, or a chrysalis.
The eggs are a different story. Especially the lurker egg in the original StarCraft, the wireframe is a lot different than the unit one. So that we all can assume it is still incomplete. And of course, why would Blizzard get rid of the egg?
As for the buildings, hatcheries turning into lairs will not have a tumor-like appearance during the process of upgrading it. It is pretty obvious through the appearance of the Lairs, it just grew tusks and that is basically it. What is the point of the tumor-like appearance just to have tusks? And if you notice, any race building on Vespene Geysers in StarCraft II, it removes the Geyser and begins the production of the structure. That is obvious of a placeholder, it is obvious that there will be a Geyser underneath those productions in the
final build.
And one last thing, the developers of StarCraft II are the ones behind WarCraft III, not the original StarCraft. They tried to adapt from WarCraft III such as the multiple building selection, idle peons, shared control (Team Melee SC-style does not exist in WC3), inventory, blink, and so on into StarCraft II. And the topic that I'm making here is pretty obvious:
You should take a look of these structures yourself.
WarCraft IIITown Hall --» Keep --» Castle
Scout Tower --» Arcane Tower
or Guard Tower
or Cannon Tower
Great Hall --» Stronghold --» Fortress
Tree of Life --» Tree of Ages --» Tree of Eternity
Necropolis --» Halls of the Dead --» Black Citadel
Ziggurat --» Nerubian Tower
or Spirit Tower
StarCraft IICommand Center --» Surveillance Station
or Planetary Fortress
Hatchery --» Lair --» Hive
Spire --» Greater Spire
Gateway --» Warp Gate
None.