Your computer is apparently struggling as Etrecheck reports "poor" performance and SSD write speeds that are about 40% what they should be. This could be due to running out of disk space or the scores of background processes you have running, including virtual machines and others mentioned below.
More details of note from the Etrecheck report:
“Configuration profiles found - This computer may have configuration profiles installed.”
Is your Mac a “managed computer,” managed by an employer or someone else? If so, that could explain some of your oddities, including the iPhone not linking properly.
“Low disk space - This computer is running low on free hard drive space.”
Low disk space (you have about 10% free, it should be at least 20% free) can cause all manner of slowness and beachballs. I’m not sure it can explain the iPhone not appearing, however.
“Unsigned Files: Launchd: /Library/LaunchDaemons/com.prey.agent.plist
Executable: /usr/local/lib/prey/current/bin/prey
This “prey” software looks like your managed computer installation, a security tool. Suggest you uninstall it to troubleshoot your multiple issues and see if that eliminates one or more of them.
I would uninstall Cocktail, Little Snitch, and Malwarebytes. Cocktail and Malwarebytes should be ok, Little Snitch has caused problems like yours for other users as reported here. Any of those three can be problematic if there was a flawed installation or they are out of date. Also, programs like Cocktail sometimes “clean” out user files that cause misbehaviors in MacOS, and if that happened an OS reinstall might be needed. They can all be reinstalled if shown not to be related to your issues. I would regardless turn off all Malwarebytes background automatic scanning, that is a known drain on Mac resources.
“[Running] Proton VPN WireGuard - version 6.5.1 (ProtonVPN AG - installed 2026-05-01) Application: /Applications/ProtonVPN.app - version 6.5.1 (ProtonVPN AG - installed 2026-05-01)”
Definitely uninstall Proton Wireguard VPN. VPNs can mess up any computer.
You have ON1 tools installed for photo editing. I am not familiar with them but might it recognize your iPhone as a camera and somehow lock it up and make it unavailable for other functions?
“Performance: System Load: 10.02 (1 min ago) 17.28 (5 min ago) 11.86 (15 min ago) Nominal I/O usage: 5.43 MB/s File system: 17.03 seconds Write speed: 1338 MB/s Read speed: 3069 MB/s”
“EtreCheckPro version: 6.8.16 (68098) Report generated: 2026-08-02 09:50:33 Download EtreCheckPro from https://etrecheck.com Runtime: 14:49 Performance: Poor”
Performance is “poor,” and your write speeds are less than 40% what they should be. Clearly your Mac is struggling, this could be due to the scores of background extensions you have installed, being loaded down by things like Little Snitch, or just running low of free disk space. Also you have multiple cloud syncing processes happening and programs like Little Snitch or the other security tools you have (including the VPN) can grind those processes down to a halt.
Given that you have other problems, like not being able to see your iPhone on the desktop and Safe Mode not working, part of me wonders if it would make sense to back up (make two backups, maybe one with Time Machine and one with SuperDuper), then erase/format your Mac following Apple's instructions at
What to do before you sell, give away, trade in, or recycle your Mac - Apple Support
then on first boot your Mac will look like a new empty Mac and you can migrate from one of the backups ONLY USER ACCOUNTS AND FILES (NOTHING ELSE) but install nothing. Then test. If all is well, you can reinstall apps one or two at a time, testing after each. By the way, this is the standard Apple solution for Macs that are misbehaving but have no hardware issues that can be identified. Before doing this, you might want to have someone at the Apple Genius bar or at an Apple Authorized Service Provider run diagnostics to make sure there are no hardware issues as this is an older Mac.
It's up to you, you can also try running uninstallers for all the above to see if the problems then go away. But you do need to free up a lot more disk space for this Mac to run smoothly.