Voxengo seem to have gotten to the bottom of this:
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It's indeed an issue with Mojave - probably due to its poor support of older API - multi-threading or older Cocoa.
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They're moving their plugins to Retina soon as well, which has seemed to fix the issue:
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The fix may be due to us moving to Retina which does not need realtime UI rescaling.
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Meanwhile, things are still quite bad with 5.963 on Mojave on my system, unless I run Reaper in Low Resolution mode, in which case things are back to being as snappy and responsive as usual, but everything is non-Retina (including plugin GUIs).