Modding and ship tonnage

[Suicide Junkie]

To a point, it will.

The AI uses a set % of its tonnage for shields and armor, but weapons will hit the slot limits, and there are only so many choices for random "extra components" to add.
For modest changes, the AI will adapt. Doubling the size of ships would require adjustments to more of the settings. (Use bigger guns, add more shield regenerators, repair bays, sensors, maybe fighter bays, etc)