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It's difficult to say which older apps will continue to work on modern PocketBook firmwares, and which won't. When my PocketBook Colour updated to a newer firmware, pbimageviewer stopped working properly because some of the necessary GUI functions were pruned from the Inkview library. Other apps that require those missing functions will also no longer work. It is probably easiest to just try them and see if they work or not. Apps that provide their own GUI code (e.g. koreader) or don't use much of it (e.g. utelnetd) will likely continue to work.
You can cross compile a lot of stuff and run it on the devices without having root. I'm not so sure about openvpn; I have the feeling that it requires kernel modules to run (tun/tap?). If those aren't already on the system, then installing a cross-compiled openvpn client on the device probably won't work.
The PocketBook devices run linux with the arm gnueabi ABI. A lot of programs from compatible linux distros can simply be copied (with necessary libraries) and run on the devices. You can do a lot of tinkering if the mood hits you.
Finally, if you are going to start pruning the supplied books, I would use the system's Library app for that (rather than connecting via USB and deleting from a different computer). The Library app knows how to update the various databases and caches on the device when books are removed, which leaves the device in a more consistent state afterwards.
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