Are you talking about the energy storage? Generally speaking, the energy storage is about double the energy output so this only applies to weapons with a fire rate of more than 2 seconds. But designing for energy storage instead of energy output for those weapons will mean that those weapons will only have a good first strike capability, but there will be less of those weapons for damage over time, as you have taken up space with more reactors.
So I guess what you mean is that for certain weapons, if you want to be able to shoot with all the weapons in one go, you must design with more reactors. Only that space is limited, so there will be less weapons. So, they don't lack weapons, they lack reactors. Well autodesign makes no sense in general, since some designs will not have enough energy for continuous fire of all the weapon, so they lack reactors, not weapons.
If you design your won ships anyways, you'll find that your designs should have less space for weapons, unless you are aiming for more range rather than more shields.