I recently experienced what I believe might be a circumstantial issue of migrating over to a new Mac machine—the 16-inch M1 Max-based MacBook Pro [sixty-four gigabytes of unified memory and a one terabyte solid-state drive], more precisely; although this is most likely software/data migration-based rather than dependent on this specific hardware, yet I've still listed my model in case it might have some interconnected pertinence to this particular issue.
❗️ Per the issue: Spotlight on macOS Monterey [stable release build 12.1] is not indexing folders properly—and more specifically, the "/Applications" folder located in the root of the macOS system tree/computer directory hierarchy.
⭐️ Solution: simply move the folders in and out of the "/Applications" (⌘⇧A) folder—perhaps to "/Downloads" (⌘⌥D)—and then move them all back to this same system Applications folder. This may also be performed by ⌘A-copying all applications inside this Applications folder (sans the stock system apps, which cannot be moved or removed in this manner), navigating to Downloads, and ⌘⌥V-moving the applications there, then navigating back to Applications and once again pressing ⌘⌥V (apps may still be on the system pasteboard, so they can be chain-moved in this manner). There may be no need to delete or reinstall the application itself, as doing the abovementioned will assumedly fix this issue, as it had in my instance. (In my case, I also rebuilt the Spotlight index right before moving them back to Applications, elaborated upon below.)
ℹ️ Note. This Applications folder is located at root in my reference above as opposed to the "/System/Applications" directory, as there do exist multiple instances with of the same folder name across the macOS base installation.
In my case, however, the following did not work:
✳️ Restarting or shutting down the Mac machine. Therefore, this is the more apt solution, as this seems like an idiosyncrasy of utilizing Migration Assistant or simply migrating your data over from your prior machine to a factory-state Mac[Book Pro] machine.
✳️ Rebuilding the Spotlight index, which can be done any number of ways, including by utilizing third-party software or by executing the command-line "mdutil" U.N.I.X.-macOS program via terminal with parameter/flag "-E" fed in as input and ran on the root system directory. More specifically, using "sudo mdutil -E /" as the Terminal command. This can also tend to beneficially repair some interrelated system information, such as system storage capacity, so it provides the correct data. (As an aside, from my discoveries, it appears to be located at "/System/Volumes/[computer name]/.Spotlight-V100" on this specific build and is inaccessible by the user with these permissions set system-wide for this item/folder; when copying the pathname, however, the directory appears as "/System/Volumes/Data/.Spotlight-V100" instead.)
I hope this helps.