Is there currently a workaround to getting this list of aliases?
Where do they get stored? If they only get stored in Zookeeper then how can they be backed up in case of a Zookeeper failure where all the config needs to be reloaded back into Zookeeper? Would I just have to recreate all of the aliases?
As far as I know, they are indeed only in zookeeper. You can see them in the Admin UI by clicking the Cloud tab, then Tree, then /aliases.json in the tree view. You should maintain documentation on how you built your SolrCloud and Zookeeper configs so you can recreate them if you lose them entirely.
A fully redundant zookeeper ensemble with three or more hosts should keep you from encountering a situation where you have to entirely reconstruct the ZK database, but but you do bring up a good point - it is always a good idea to have actual backups in case of severe bugs, human error, or malicious intent.
Here's some information at the zookeeper level on maintenance and data file management:
I found these URLs in a Stack Overflow question about backing up zookeeper: