You won't have to worry
Minion knows the Versiom number you gave on ESOUI.com ,as long you don't change that yourself,
Minion will not "detect" an Update.
When you install an Addon ,minion will "remember" the Version it installed, and will compare it with the data from esoui.com
Also as a precaution, i always update every addon by hand and not using the "Update all" functionallity.
Only this way i notice if something changed in other addons anyway