your Mac (since OS Catalina, I believe) will read the NTFS drive but it can’t write to it, which can pose problems down the line, if you want to install something new on that drive.
If you must keep the drive NTFS formatted, there is 3rd party software that can help with this.
I would simply copy the data to another drive temporarily, format the SSD drive to APFS, then copy the data back. Unless you need to access the drive from a PC as well, then I would choose exFAT.
setting up two different HH controllers via two different modules, connected to one instance of SD3 will not work, if you expect them to act independently.
If you, on the other hand, wish to connect a 2nd HH controller to your module/SD3 instance to be used as a “regular” pad, it should be just as easy as adding any other pad. Make sure it sends unique notes to SD3 and ‘Add Instrument’.
You started by Enabling the Roland TD-30 MIDI Preset on the MIDI In/E-drum Settings page  in SD3?
Which Library and Preset are you using?
Do you wish to change the sound of Cymbal 5 to the one loaded on Cymbal 3? Or is it only the triggering that is wrong?
Do you have the TD-30 @ Factory Settings MIDI note wise?
The SD3 software does not split the incoming MIDI to several Instruments, so if two Cymbals are triggered, the most plausible cause is that your module is sending two notes. You can expand the MIDI Monitor Property Box or open the MIDI In/E-drum Settings page and watch the Analyzer to see which notes are received from the module when you hit the Cymbal pad.
as you have noticed, when you de-select notes after editing them, they are considered “done” (unless you Undo, that is), so you may keep editing; e.g. adding Swing, Quantising some of the Nudged, Swung notes. I do not know if it is possible to add the ability to have all individual note original and edit values remembered but I imagine this will be tricky to implement if there’s a lot of individual editing throughout an entire Song.
Anyways, I’m not a programmer, so please feel free to add this to as a request in the Requests & Feedback section.
of all the libraries I have installed on my drives, the only time I have seen ‘Side’ Mics are if there is actually a Side Snare, to the left of the main Snare.
Top and Bottom Mics, the odd Stereo Mic and some effect versions of the said but never a microphone for the sole purpose of capturing the side of the snare.
I am pretty sure this is not something dictated by Toontrack, since every library engineer would make the decisions in the studio.
