Just updated my 15" Retina early 2013 Macbook Pro to 10.13.2 from El Capitan and immediately noticed slower boot. I have an OWC SSD in place. I had backed up El Cap to the original Apple module, updated to HS, reinstalled the OWC and then I could install HS on OWC module.. :-(
I've had been running Disk Sensei for Trim with El Cap.. With it turned off, my boot time is as fast (if not faster) than with El Capitan... With Trim turned on in Disk Sensei, I get the extended start up. Once things are up and running, everything seems to be at normal speed, so not sure which is a better solution.. Faster boot and no TRIM (thought APFS somewhat eliminates as much of a need), or slower boot and TRIM??
1) check if your OWC SSD really support TRIM (some of them do not), if NOT, then disable it. Enjoy the normal speed.
2) unless your daily usage is mainly keep rebooting the Mac. Then usually slower boot with TRIM work better.
3) if your Mac shows another abnormalities, then keep TRIM disabled may help. In my case, TRIM can cause Finder micro freeze. Or even an internal HDD disappear after warm reboot (only in HS).