Is it possible to return to Skuldafn

Even though you can kill their guardians and get a Cleared Map tag under the location, exterior Word Walls will eventually respawn, both Dragon and Chest.

If you crisscross across Skyrim via Fast Travel, you should get more than enough Dragon Bones / Scales from previously cleared Word Walls that have since respawned.

If you're still looking for more dragons, you can still use the Word Walls, just wait for an in-game week (or however long it takes) then repeat your circuit across Skyrim.

Mallus Maccius not being available as a fence is a known bug.
According to UESP:

Mallus Maccius may not have the option to sell merchandise after completing Dampened Spirits, despite offering to provide fence services to you. Instead, at odd hours of the day, he will respond as if the player is disallowed from entering the building.
A possible fix for this is entering the Meadery through the basement.

Of Niranye a similar bug is not registered on UESP.
It does state on elderscrolls.fandom.com, however, that the mission Summerset Shadows must have been completed (which is not a necessity for completing the main Thieves Guild questline), and that she mustn't have "fought" (turned hostile towards the player, I presume) in the process.

Since, according to its description, it only "adds a very large basement connecting all houses in the game", it is unlikely that Dovahkiin Hideout has influenced the fences in Skyrim. Nothing about it is mentioned in the mod's thread on the nexus.