It wouldn't surprise me if it processed vulkan shaders briefly every time, to check for recently used ones and upload them to Steam.
If it's taking more than a few seconds every time, I would guess that either your last play session triggered a bunch of new shaders (for example if you explored a new area that used different visual effects), or you've stumbled upon a bug.
If you think it's a bug, you should consider checking for reports on Valve's issue tracker entry for that game, or on the Steam for Linux issue tracker if it affects many games. If there are no reports already, consider creating one.