I don't think the Thalmor are bored, in fact they're quite busy hunting and torturing civilians. Cowebs are the least of their worries.
And if you absolutely have to, have the decency to compare with one in a war theatre (like Northwatch keep). I guarantee you that American bases in France and Germany during WWII and bases in Vietnam during the conflict of the same name had "cowebs" in corners, and worse things. I'm sure the forts in Summerset Isles are cleaner, like army bases in the US are cleaner.
Finally, it looks to me like Northwatch Keep is just an abandonned fort recently taken over by the Thalmor as a base of operations for their torture missions. I don't think they've been there for ages...
Well they do guard the Fort all day. They are the ones assigned to the fort, who have to live there. No one wants to live in a filthy environment. Filth breeds disease. In a siege one would have to live in such a fort for weeks or possibly months on end. Disease would kill everybody off within a week if it wasn't kept excessively clean. Besides that, there is no way that could be posted there for weeks and months without getting seriously ill.
I doubt the fact about the American French/German bases during the war and afterwards - I think you don't appreciate exactly how old, disciplined or organised the military is. The human race has had an organised military for at least 5000 years. Look at the Ancient Romans, the armies of Alexander the Great, the British Empire and other armies of that era. The comparison is apt. They wouldn't have survived if they had set up camp for months on end without keeping it livable.
Who are the Thalmor at war with? They aren't at war with any faction in Skyrim. They've also been in Skyrim for 25 years (Since the Markarth incident)
Would General Tullius invite the Emperor for an investigation of his forts, only to show him a skeever infested hole? Likewise, would the Thalmor in charge of Northwatch would invite the ambassador for an inspection with it in its current state?
You underestimate how much cleaning a group of motivated people can do in a couple of hours.
What I also don't understand is why the principal base of operations of a hold for each faction is a temporary camp, often sitting in the middle of a field, and often at a tactical disadvantage to an attacking force.
Not to mention the forts that are located so that a besieging army would have the advantage. (There are a few up north where the fort's battlements are below a hill less than a bowshot away, allowing a group of archers to pick off every soldier manning the fort, while they have to charge up the hill and fire bows against gravity)
Or like you say, no fort in the game has a permanent garrison. All appear to have displaced the previous occupants (and the forts must have been occupied), yet the previous occupants weren't dug in deep enough to avoid being displaced (Whereas the foresworn in the reach have been entrenched in redoubts there for 25 years)
What gets me about that is Fort Greymoor. Fort Greymoor is right next to the busiest trading hub in the province and is not only a strategically important site for a Whiterun garrison, but is also a mass of freely available stone that could be used for building materials/trading materials to other places in the province, as happened historically. Yet the initial occupants are a group of bandits, and the fort changes hands regularly without Agnis even noticing. You've have thought the city guard would have cleaned out the fort because of the risk to merchants and either occupied it or torn it apart to repair damage to the city stonework (or that someone would have just torn the fort apart and sold it in the aftermath of the Great War)