This is likely because if you click on the shortcut, you don't just bring the minimised application to the front but rather try to launch the program from scratch. Joplin doesn't allow running multiple instances like that, so during the process it sees the already running instance, abandons opening a new instance, and then brings the already running one to the front. All of this requires processing power.
If you click on the minimised icon, you just bring the already running Joplin to the front, which doesn't require any processing power and thus is instant.