Hey Zomblue. Sorry, I just saw this. Seems like you aren't the only one with this issue. I found some trouble shooting but want to see if I can narrow this down to an update or some other software glitch. Has it always done this or did it start doing this after a system update? From a quick Google search, after the new major update, people reported slowdown.
What you can do to start is rebuild the database. Some people report that this fixes their problem, some people it didn't. Its a good place to start. It should basically clean up the crap the system gathers over time that slows it down (like how Windows slows down, lol). See instructions below.
1) Turn off the system, don't put it in sleep. Has to be powered down.
2) To turn it on in safe mode, hold the power button down. Don't let go until it beeps twice. It'll take a few minutes.
3) You'll see it boot into safe mode with several options. You'll select option 5 for Rebuild Database. It'll say it takes several hours, but I've never had that happen. Usually a few minutes but could take longer depending on how much stuff you have so be prepared. Also, whatever you do, don't select any of the Initialize options by accident. You'll lose all your data
If you are leary about losing data, you can always back up to a spare hard drive before hand (which honestly is just good practice). Here's the link. If you backup, just note trophies don't back up. I've backed up and restored my systems a lot in the past and lost them every time. But, I also don't give a rat's tookus about trophies so I didn't care
One thing to note about using external hard drives. Most hard drives today are formatted to NTFS for use in PCs. The PS4 uses FAT formatting, which PCs don't really use anymore (but can read just fine). So you more than likely will need to reformat the external hard drive before backing up the PS4. If you don't know how to do this, let me know.
https://manuals.playstation.net/document/en/ps4/settings/backup.html