Okay so I have had this issue every now and then, when it comes to talking to non-essential NPC's that i dont care about, i can talk to them no problems. BUT, NPC's i need to talk to for quests, my cursor would disappear on him (i use iHud) and then no option to interact. While reading this forum i found out that actually taking my shrouded cowl off brings back the option to talk to him. Now i found what actually finally fixes this. It is in fact got to do with the Sneak Tools mod. I went into the mod configuration menu -> sneak tools -> then activated the "menu pop-up" option. Sneak tools thinks that while you have a cowl on with identity hidden, that you're trying to assassinate someone, so you gotta activate the menu pop ups while you're wearing sneaky stuff.