I wonder if it's connected somehow with that occasional bug many of us have seen with vendors, where they refuse to staff certain shops. I've had some shops that are never open, even though there is an empty staffroom nearby. Sometimes when I hire a new vendor and drop them next to those shops, they'll simply walk away. Also, the thing with staff insisting on walking all the way across the map to a staffroom, even when there's more than one much nearer to them. This even happens occasionally when I've carefully set up work zones.
In those cases either firing the offending staff member and hiring a new one, or in the case of the food vendors, deleting and re-placing it, can solve the issue. But it sounds like the issue with the modular shops is persistent. Reminds me a bit of a bug I had in one zoo where a vet was just standing in the flowers outside a particular habitat, and I couldn't get him to leave, even by firing him or demolishing said habitat. In that case, though, there was a dead tapir he wouldn't remove whose ghost was "haunting" the guests in that corner of the zoo (misregistered as an escaped animal).
There's another weird glitch with those food counters, where the staff member always starts to walk off when you drop them in front but then they do a U-turn and come back. Once in a while, however they just keep going. Sometimes it's due to placement, but it's interesting that they never go straight to the counter, even when they end up staffing it.
The shop thing has always been an aspect of the game that feels hit or miss to me. Why are some food vendors overflowing with guests, but the one next to it gets no one, for instance. And why are the guests always hungry and thirsty, even when there are tons and tons of food shops (far more than in a real zoo), but some are empty of guests? And why do the guests have to eat more frequently than shrews and hummingbirds IRL? Is it a way the game augments player income?