Mac Mini hardware test

It depends on the exact model of your Mini and the OS installed on it. If the Mini has (or had ) macOS 10.12.6+ installed, then you should be able to access the online Apple Diagnostics. Keep in mind the Apple Diagnostics won't detect most drive failures.

Does your Mac boot either normally or into Safe Mode? If so you can run DriveDx on the drive and post the report here using the "Additional Text" icon which looks like a piece of paper. If you cannot boot macOS, then I can provide instructions to create a bootable Linux USB drive that can check the health of the hard drive. Reading the health information (aka SMART attributes) directly from the drive is the best way to assess the health of a drive.

If you want to look for possible software causes for your Mini's issues, then run EtreCheck and post the report here using the "Additional Text" icon which looks like a piece of paper. The contributors here on these forums can examine & interpret the report for you by identifying any software that is known to cause problems.

Sometimes Etrecheck will report the slower 5400rpm hard drives as failing, if they are writing and reading slower than normal.

The biggest problem I see, is that you have Sophos installed on your Mac Mini.

Uninstall Sophos as per the developers instruction.

Startup in Safe Mode, followed by a normal startup.

Then run and post another new Etrecheck report.

Your hard drive is just worn out as indicated by the 1% Warning of the Load Cycle Count. The RAW value is 2.6 million where the usual life expectancy from the manufacturer is around 800K to 1M. Much of this Load Cycle count wear is due to macOS constantly sleeping & waking the hard drive. But even so you did get an impressive 23K hours of run time out of this hard drive which is somewhat rare for a 2.5" hard drive even installed into a desktop system.

You need to replace this hard drive. I would recommend replacing it with an SSD as that will give you a really nice performance boost.

Also take @den.thed's advice about not using anti-virus software.

Make sure to have frequent & regular backups. It is impossible to recover accidentally deleted data from an SSD plus an SSD can fail at any time without any warning signs.

Removing Sophos did help with the hard drives I/O and Read/Write speed.

1st report

Performance:

System Load: 1.33 (1 min ago) 1.26 (5 min ago) 1.22 (15 min ago)

Nominal I/O speed: 0.82 MB/s

File system: 151.36 seconds (timed out)

Write speed: 39 MB/s

Read speed: 66 MB/s

2nd report

Performance:

System Load: 1.35 (1 min ago) 1.66 (5 min ago) 1.65 (15 min ago)

Nominal I/O speed: 3.30 MB/s

File system: 121.80 seconds (timed out)

Write speed: 52 MB/s

Read speed: 72 MB/s

Safe Mode can take up to 10 minutes or longer on a Mac that came with a slower hard drive. It pretty much does the same thing as running Disk Utility > Repair while startup in macOS Recovery.

macOS does not need help protecting or cleaning itself. Third party AVware and Cleanware are not needed or recommended in macOS. They will do nothing for you except slowdown your Mac at best, and/or cause all sorts of other issues up to and including borking your machine.

You need to replace the hard drive since it is worn out. On drives with bad Load Cycle Counts I have encountered performance issues and other odd drive behaviors. I guarantee you that the hard drive is causing the majority of your issues with Sophos just adding to them.

Just don't install any anti-virus, cleaning apps, or third party security software on the Mac when you replace the drive. Anti-virus software hooks into the OS at a very low core level so if the AV software has any issues it will affect macOS at its very core. For what it is worth I don't recommend anyone to run third party AV software on Windows anymore (use Windows built-in AV instead) as the AV vendors (even once respected ones) are just producing crap privacy invading apps with some selling vendors your personal information.

You may not notice the performance issues as much on a 2018 since the system and SSD are much faster than the older systems. If you ever feel you need to scan your system, then use the free version of MalwareBytes (no need to install the driver for the real-time scan), but even this should not needed if you practice safe computing habits.

You're welcome. Awesome, hang in there. Me, I turn 65 next weekend.