I believe that offering "mini cargo bay extensions" (something like +1TC of cargo space for 10t of equipment space) would solve those issues
Just thinking a bit more about this, I'm not sure about the best implementation. I'm hesitant to create something that allows the player to increase their cargo space over the default maximum for the ship class, as it would potentially discourage the player from ever wanting to update their ships.
Slightly off-topic, but this OXP kind of does it already. If you quickly look at the differences between Cobra I, II, II-XT, III and III-XT for instance, equipment upgrade OXPs kind of blurry the lines and you think twice before buying a new ship, especially when one considers the credits invested in equipment and the credits one loses when selling the current ship (I've already whined about it in "Suggestions"). So when one considers a new ship, it usually belongs to another class.
Sometimes I wonder if it would be better to suppress most of the traditional equipment upgrades (naval grid, military shields, etc.) to make the ship market more interesting (for instance one could get a Cobra with passenger berth only from the market and/or ship OXP makers could offer many unique variants with sensible parameters according to the fitted equipment). But something tells me it won't happen any time soon.
Coupled with this is the inherent difficulty in expanding the cargo space of ships beyond their default, where startup sequences can result in cargo being lost.
Too bad... If we cannot kill our two birds with that one stone, then maybe it's not worth the complexity. Currently if I want standard injectors I have to downgrade two other equipments to keep my cargo space. I believe that few would want the lesser injectors (even if maybe they aren't that terrible), so I think starting at 1t for standard injectors is good enough.