Ive never played an elder scrolls game before, xept skyrim, and was wondering how the series handle the player made choices in a game regarding lore for future games?
Example, shouldnt next games contain lore about the victory for the imperials/stormcloaks? Or will stuff like that just be forgotten?
Same thing counts for the assassination of the emperor. Would be weird if they wouldnt take that in account.

Everything will.

I think Titus Mede II will be assassinated, but it won't be said who did it. Same with other main choices.
As for the civil war, I'd say it's going to be dealt with as vaguely as possible so both sides can essentially claim victory.

Things should continue. Some parts of Morrowind continued in Oblivion and Oblivion did somewhat continue in Skyrim. Dragonborn holds a lot of lore for Morrowind's Bloodmoon.