Ministers can and will upgrade both ships and facilities, IIRC. However it would tend to be a bad idea to do it all immediately, so it takes its time. Upgrades only happen to ships which happen to be at a space yard when the minister (occasionally) decides to do it.
In the construction que window there is the option to UPGRADE. Click this and any available upgrades will be placed into the cue.
Also under the MINSTER controls you can turn on the Retrofit minister.
Retrofit = Upgrade.
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Creator of the Star Trek Mod - AST Mod - 78 Ship Sets - Conquest Mod - Atrocities Star Wars Mod - Galaxy Reborn Mod - and Subterfuge Mod.