Covid seems to be a factor, but the Madame Tussauds nearby is open. The Dungeons does have a lot of fixed costs, which could be an issue. The Blackpool Dungeons sometimes closes misweek, presumably for a similar reason.
Nonetheless, The San Francisco Dungeon opened in 2014. If it were that successful, they'd probably have announced another one in the US by now. Although not being successful enough to announce another one doesn't mean it wasn't making money. It could just mean that they get a better a return on one of their other midways. You're right, it could just be SBNO. But assuming they're leasing the site, how long is it going to be viable to keep it closed? Of course, the flip side is that we don't know when their lease expires. It might not be easy for them to move out.