In a tweet from Pierre-Loup Griffas, a Valve developer, he gave some information about an unmentioned addition to the recent Steam client update. When removing Non-Steam games and apps, Steam will now clean up all related files including shader caches and compatibility data created by Proton.
This is a great quality-of-life change that applies to both Steam on desktop Linux, as well as the Steam Deck. There should be no more need to use third-party tools or manually cleanup things like shader caches which can start to take up a lot of storage space. This is especially convenient for Steam Deck owners with smaller SSDs.
Steam's recent client update came out earlier this week on June 14, 2023 with slew of changes. Most notably an overhaul to the in-game overlay, giving it a new UI and cool new notes feature. Having used it for a couple days now, it's pretty slick but does still have some lingering issues on Linux from the beta period. The biggest of which still seems to be very poor performance in Big Picture mode for Nvidia users. Hopefully Valve will take some time to polish the experience for Linux users.