There is actually an open source eReader, openbook https://www.oddlyspecificobjects.com/projects/openbook/
Unfortunately, the current screen it uses is not being made anymore. People have stated that they have gotten other screens to work, but no official instructions on using them yet
It is probably an old case design. In the early water cooling days, there would be separate watercooling units that sat outside the case. The grommets were so you could pass your tubing through.
I wouldn’t really worry about the dust tbh, you will wind up having to clean it regardless.