MIddle click hasn’t been intentionally disabled. To fix another bug (on Mac) accidentally broke middle click/paste on linux.
There is the other issue that middle click on linux is itself very broken (even when it was working) https://forum.obsidian.md/t/linux-middle-click-paste-is-problematic-and-needs-to-be-automatically-disabled/34717.
The middle-click/clipboard paste will be reworked in 1.0.4.