Is there a way to compress the traffic going across an EoiP tunnel?
unfortunately no.
Will IP Packing work over a EoiP tunnel?
If you’d be using the EoIP tunnel only for IP traffic, why would you need an EoIP tunnel?
To answer your question, packing should work, as an EoIP interface is like any other L2 interface from this perspective.
Also you need to remember that compression of network traffic is becoming less and less effective as most network traffic is encrypted or already compressed.
E.g. in the past I had good results with compression of generic LAN traffic between offices, carrying e.g. SMB traffic which would be Office documents.
Using LZX compression on PPP links would yield a compression factor of 2-5.
But today office documents (.docx, .odt) are already compressed! So this is no longer compressible.
Similarly, HTML traffic is very compressible, but today it is usually carried over TLS (https://) which makes it incompressible again.
So when you get compression working, the results may be disapppointing.