While I was at Google, instead of having multiple .so files, the main launcher was a C++ binary, and all external C++ dependencies were linked into it (that's it if you have the source code), then you didn't need that.
I guess now it's up to the BUILD system to achieve that, where if you have more flexible BUILD language you can instruct everything to go in the main launcher file, then have all the .jars into one, slapped at the end of the file.
At the end, ship or update only one binary to your service, desktop machine, etc.