I see you are not familiar with git diffs.
What you do is you go to your WoW\Interface\AddOns\!Questie\Modules folder. There you open the QuestieNotes.lua with an Editor (I suggest using Notpad++, it is great and adds a menu option for opening files to the windows right click).
Then you go to line 560 and add "--[[" (without quotes) in front of the "for k, v in pairs(QuestieMapNotes[c][z]) do".
Then you go to line 595 and add "--]]" behind the "end".
Repeat this process in line 712 (before "MMIcon = Questie:GetBlankNoteFrame();") and line 726 (behind "table.insert(QuestieUsedNoteFrames, MMIcon);").
This comments out (deactivates) the code that would otherwise create minimap icons. If you decide to switch to some round minimap you can remove the dashes and brackets and the icons will be drawn again.
By the way, this is a know issue with non-circular minimaps and with Questie development being stalled at the moment I wouldn't expect a fix anytime soon. So it's either round map or no minimap icons.