My final post on the original topic: long startup. Turns out my Samsung T5 SSD died but rose from the dead: while 1.2 TB of data disappeared because the encrypted APFS volume refused to mount, it did reformat without a problem and an extensive R/W test shows that all is well with the hardware it seems. So I don't know whom to blame for this: Samsung or Apple's APFS, or the combo.
What does this have to do with the original thread you're asking? After resurrecting the SSD, whether I formatted as HFS+ +/- encryption, or APFS +/-encryption, Xojo startup with a full set of MBS plugins completes in <30 sec.
So I am at a loss to explain the previous slowdown. The only diff is before, the SSD was formatted as APFS+encr under high Sierra, vs now I moved to Mojave. So it wasn't the encryption, or HFS vs APFS.
I am still left wondering whether APFS is what pooched the SSD in the first place...Has anyone had issues with APFS? I am reluctant now to use anything but HFS.