I keep getting a popup asking if I want to delete stuff from old version of emclient, to save space. If I say yes, what will it delete? System stuff or my old messages?
It will delete entire database of v6, stored messages, settings, account settings etc.
If you are not sure what data do you have stored ther do not delete them without knowing what exactly you are deleting.
Messages stored on server should be synced back to eM Client but this is individual and I cannot guess if there are any messages you need or not, it also depends on account configuration(POP/IMAP).
Best thing to do is either leave those data on your computer or backup them and then delete.