Standard Linux distribution packages are just a bunch of files in an archive that get extracted and configured during installation and partly or fully (with configuration files via --purge option) removed during uninstallation. That's why uninstallation is also called removal of packages.

Apart from ususal hard drive wearout and growing package manager log files, which are automatically compressed and deleted after some time (see Linux Log Files and logrotate), nothing happens.

After all it seems only logical, that you can't break much by moving or deleting the same file repeatedly over and over again.

With the arrival of affordable consumer SSDs, delay in data retrieval or crippled performance and throughput caused by suboptimal data placement on platters also has become more trivial than before.

One thing that can break are dependencies, but that can also be fixed.