See: https://forums.kronosaur.com/viewtopic.php?f=3&t=7465&p=66905#p66905
Based on the graph in the OP of said forum, and conversation on IRC.
The current system of increasing WMD ratings as the level increases *and* increasing base damage as the level increases results in a rather problematic progression system.
This may be one of the reasons why internal compartments pose such a great problem. By making the trend more linear (or at least matching the general curves of the game better) by removing the level from consideration when deciding on the WMD rating of a weapon, this may make compartments (and early-game multihulled stations) less problematic to players. However, this would likely cause issues with wreck HP, and potentially overcorrect the issue and make compartments underpowered.
Edit: 2/1/2016, altered title a bit, rephrased main paragraph.
Making WMD consistent with the kind of weapon rather than weapon level is a good idea, but internals have issues beyond this. For example, striking a station with a fast beam weapon will kill it about as fast as bombarding it with a howitzer or missile launcher.
I'd suggest making missiles and short range explosive weapons have higher WMD damage than howitzers in order to make methods of dealing WMD damage that aren't howitzers actually competitive(right now, ammo weaponry isn't worth using against damage sponges like stations and large capital ships, and howitzers are unrivaled for destroying stations, due to the ability to hit from beyond the range of defenses), and modifying compartments so that fast non - WMD weapons are decisively less effective than weaponry that one would expect to hit hard against compartments.
Edited ticket slightly to clear things a bit.
I agree with this—WMD should be related to weapon type, and there should be WMD:7 weapons at all tiers/levels.
For 1.7 Alpha 1, I've made a change to the WMD algorithm. First, all weapons now do at least 10% damage using a stochastic adjustment. For example, 1 HP of laser damage will do 0 damage 90% of the time and 1 point 10% of the time. Previously, we would always do a minimum of 1 point, which skewed the WMD rating of low-level, high-fire-rate weapons.
I've altered the curve. The scale now looks like this:
WMD 0 = 10%
WMD 1 = 25%
WMD 2 = 32%
WMD 3 = 40%
WMD 4 = 50%
WMD 5 = 63%
WMD 6 = 80%
WMD 7 = 100%
I've also added more WMD, particularly to low-level ammo weapons, so we should have a more even distribution. See: https://ministry.kronosaur.com/record.hexm?id=30518