Whether islands are depicted on maps or not is somewhat inconsistent. The biggest example is probably Solstheim. Solstheim didn't show up on any maps and was never referenced before Bloodmoon, then dropped off the maps of Tamriel again in Oblivion, despite the odd Bloodmoon reference, then reappeared again in Skyrim. Unused Oblivion dialog has, "Wonder why Solstheim wasn't on the old maps... not that anyone should care." This could be a poke at the fans, but it could also mean that cartographers are in the bad habit of not including uninhabited islands or islands that they deem unimportant, which could explain why Bleakrock Isle doesn't appear on any third and fourth era maps.
Also note that the game world isn't a 1:1 correlation to what would actually be there, excluding Daggerfall (which has a gameworld bigger than Britan, but mostly filled with randomly generated material.) Bleackrock Isle probably is still there in-universe, it just wasn't noterworthy enough to be shown in Skyrim.
Also, ESO launched in 2014, while Skyrim was released in 2011. That might have something to do with it too.
I would guess that some time after the Daggerfall Covenant sacked the island, it was claimed as part of Morrowind, perhaps along with other areas of the northwest. That said, it could be inhabited by Nords anyway, like Dagon Fel.