The time it takes to encrypt is proportional to the size of the data, plus some constant overhead. You can't save time for the whole operation by splitting the data, except by taking advantage of multiple cores so that it takes the same CPU time overall (or very slightly little more) but less wall-clock time. Splitting can of course be advantageous if you later want to access part of the data.
GnuPG compresses data before encrypting it. If the data is already compressed, this won't do anything useful and may slow the process down a little.
I recommend duplicity to make encrypted backups. It takes care of both collecting files and calling GPG and it knows how to do incremental backups. It splits the data into multiple volumes, so it can save wall-clock time by encrypting one volume while it's collecting files for the next one.
The first time you back up 50GB is going to be slow regardless. If you have AES acceleration on your hardware, it helps (as long as you make sure that GPG is using AES — GnuPG used CAST-5 by default before version 2.1, but it uses your public key's preferences and that should default to AES even in GPG 1.4 or 2.0).