“Some” as in dozens (for my apps, at least). It’s a solution, but not a great one. The projects I depend on will have to remove such usages eventually to avoid awful UX (and avoid punching holes in encapsulation).
For server application, this is a one-time administration effort. If you are concerned about `--illegal-access=allow`: yes, you should strive to get rid of it before security auditors blow an artery because of it.
Desktop applications are usually not delivered as bare JARs, but with wrapper binaries or scripts, where such flags are supposed to go.