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So to wrap up this thread. I have been working with Synology on this and it turns out there are no resource limits per se that I am hitting. They do have a limitation of 10,000 sub-folders per folder if you want to view the files from the web gui built into the unit. That doesn't apply to file systems mounted on other computers.
Over time Calibre builds up a file structure that doesn't match the expectations of other file manipulation software. So while I haven't hit any limits, dealing with many 10s of thousands of tiny files (i.e. subfolders) contained in a single main folder can have an impact on performance. For example a full backup of the Calibre directory from scratch (i.e. empty disk) takes ~2 weeks. A year ago it was more like 2 days.
So I will probably try the column hack at some point after things settle down a bit.
Funny I thought I would be hitting limits on the embedded database before I hit basic file system limitations.
As far as settable OS parameters there is very little that can be changed once the volume is created.
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