This solution works for me but I need to update the file after every update.
I think I found the solution this morning on ubuntu 18.04, Gnome Shell 3.28.4
Add the icon to hicolor theme
sudo cp /snap/gitkraken/current/usr/share/gitkraken/gitkraken.png /usr/share/icons/hicolor/512x512/apps/
Update the icon cache
sudo gtk-update-icon-cache -f /usr/share/icons/hicolor/
Reload the desktop
nautilus -q