As a reminder you did start by saying that you updated Kodi and then had issues.
I really don’t know why you must assume the issue is on Yatse side, Yatse have way less bugs than Kodi.
With that said:
Yatse logs properly shows the commands being sent
2021-02-05 17:57:34.673 Verbose/EventClient: sendButton(R1,volumeplus)
2021-02-05 17:57:35.239 Verbose/EventClient: sendButton(R1,volumeplus)
And kodi logs shows that the event are received and are the proper ones.
2021-02-05 18:40:57.120 T:1937100208 DEBUG: HandleKey: leftctrl (0xd0) pressed, action is VolumeUp
2021-02-05 18:40:57.837 T:1937100208 DEBUG: HandleKey: leftctrl (0xd0) pressed, action is VolumeUp
So as said, either you have enabled passthrough on Kodi, or have broken keymaps or other Kodi side configuration issue.
You can edit Yatse host and disable event server there to workaround keymap issues. But it will still be a Kodi side issue and will prevent some functions to work properly.