So, I'm revisiting this since upgrading to v17.
Now I'm seeing the following logs being written to the C:\Program Files (x86)\SmarterTools\SmarterMail\MRS\App_Data\Logs folder.
DebugLog 2019.07.10.txt
SignalRLog 2019.07.10.txt
2019.07.10-SharePoint.log
ErrorLog 2019.07.10.txt
2019.07.10-bosh-xmpp.log
Some of the other files, previously reported, are now being written to my correct log directory (S:\Logs).
It's possible to copy historical log files that are now being written to the correct folder (i.e. EWSLog 2019.01.12.txt) and this doesn't break searching the logs within the web interface.
However, the auto-compression of these log files doesn't work anymore. This appears to be caused by the name format of certain files being changed.
Taking the EWS log as an example, I have 300+ log files (over 340GB) in the C:\Program Files (x86)\SmarterTools\SmarterMail\MRS\App_Data\Logs folder. The format of the filenames is EWSLog 2019.01.12.txt, but SM is now writting these files to the correct logs folder and naming them like 2019.07.10-ews.log.
So, I copied all of these old EWS log files to my correct log directory and then ran the following Powershell script, which renamed all the files for me.
Get-ChildItem "S:\Logs\EWSLog*" | Foreach { Rename-Item $_ ($_.Name -replace "EWSLog ", "" -replace ".txt", "-ews.log") }
Now these new files will be compressed when the daily maintenance task runs!