This is an long term issue, but it should be resolved somewhere in future

Eventually, saving structuredata for any reason will become a bottleneck in server's work, because file will grow >50 mb, casuing huge lag (>10 seconds) when Recurrent Complex save it's data (sometimes lag even bigger than jungle maze generation). Disk is not a bottleneck - server (Linux based) runs on SSD.

Edit: Maybe store dat files per region? (32x32 chunks)

Would second this, helping run a big server and tracked down a regular crash happening due to the server running out of memory trying to read a 161MB structuredata file. When I tried opening it in NBTExplorer it was well over 4GB uncompressed.

Yep, per-region (or per-structure? hrm) storing is the way to go. I will tackle this some point after the other issues are through.

Workaround btw is deleting the structureData file. It contains stuff that's important for structure generation and can mean structures at the edges of your world are cut off, and /#whatisthis will fail on old structures, but otherwise it has no real downsides.