So, today I want to present a number of ways modders can balance mods without resorting to direct nerfs. These balance methods mean that modders can keep powerful weapons, but add a certain characteristic to make them less brain dead easy to use.
Door placement
Doors are essential to most parts, but it's interesting how few modders know how to use doors to their advantage. Doors can make the placement of a part quite challenging. A good example of this is the stock missile launcher. Since the missile launchers doors are on the side, it turn a rather overpowered weapon into something much more interesting to use. Since you can't slap it down anywhere, and you need to plan ahead. Modders can use this to their advantage, by making more powerful weapons also have more unique door placement, to challenge builders to work around this issue.
Size
Bigger parts are harder to use, but also boast more power. Larger parts feel more obligated to meet their expectations in power. A very powerful cannon should be much bigger relative to their smaller counterparts, and is justified to be such. In summary, make more powerful weaponry bigger, so that they are both more difficult to place and simply more interesting.
Drawbacks
Weapons have different drawbacks. For example, the large cannon is very powerful, but it's slow moving shells and poor accuracy mean it's situational to function best versus larger ships, but performs horribly versus small ships. Modded weapons could also use this formula, by making their weapons perform best in different situations.