specific questions

[Suicide Junkie]

1) You will need to make sure that the real destroy-planet components are available first, or at the same time. Otherwise the AI would see the destroy planet ability and try to use it on its ships. It will use the highest ability amount when it has the choice though.
The mines will probably blow these up just fine though.

2) Yes. Mine damage stacks just like regular weapons in combat. Weapons that do not stack include the "only X" damage types. Normal and X-skipping damage will stack.

3) Set the ship design obsolete. Click the "hide obsolete" button in the design screen.
Each year (10 turns) the game will check to see if there are any ships of obsolete design still in the game. They could be yours, or in enemy hands. If there are zero examples of that design left in the game and the design is marked obsolete, it will be deleted permanently.

4) Yes, for fighters explicitly added to a fleet. Launched units will not gain a bonus from their mothership as far as I know.

5) Possibly. You would have to mod in a tiny max-exp component and try it in the game.

6) It depends on what the ability type is. For those that use the second argument for stacking restrictions, like bonus movement, the second arg is what matters.
For others, like ECM and combat sensors, it is the family number that determines if it will stack or not.
Some, like shields always stack.
And some, such as emissive armor, never stack.

[Alneyan]

Oh, a clarification: I thought question 3 was about making the size of vessels disappear, not designs. If you meant designs, SJ is perfectly right.

[Frederick_d_Ohlmann]

For the first : to be clear I want to do warhead "planet destroyer only" and all stellar with this ability.

And for the 3 it was *not* design. I have a mod with 48 size of ship and it's a pain to find the good one.

Anyway, thank for the quick replies.

[Suicide Junkie]

Frederick_d_Ohlmann said:
And for the 3 it was *not* design. I have a mod with 48 size of ship and it's a pain to find the good one.

Hull sizes do not get obsoleted.
You need to simplify your set of hulls, or perhaps have a clear ranking of them such that the best ones are at the top or bottom of the list, or are otherwise easy to find.