Hey there,
I am really sorry for the delay of this reply as it is a weekend for us here.
A - Why the ea pre-created templates don't show on the dashboard>templates>templates display when using super user access like your own screenshot shows? It would be simpler that way.
Currently those core template only can manage by the owner which is your original site admin.
http://take.ms/UH5b8
I will discuss with the team regarding this and see whether we can change this behaviour in next version.
B - On myphpadmin can I simply delete or unpublish each system ea-template? I tried to change the system field for each to zero, but no succes.
You can simply delete those core template from this table #__ea_templates , it will not affect any other thing.
and I will discuss with the team regarding this and see whether we can change this behaviour in next version.
C- When the system ea_templates are deleted, will new EA version updates reinstall them?
It will not install back those core template when you update to next version.