Because there's already too few exploration tools in the game, to the point where you can fit everything you need in a Hauler, and still have a slot left over for an optional extra. With this change, there are now even fewer reasons to sacrifice jump range for more optional modules slots, meaning that "do everything" exploration ships won't have to sacrifice jump range for utility. This in turn means fewer interesting decisions that need to be made during outfitting, and that means fewer interesting decisions will need to be made out in the black as well.
For example, the basic exploration Hauler can't equip both Shields (making landing on planets much safer) and an SRV (can only be used after landing on planets) without sacrificing necessary exploration equipment. Now there's no need to choose.
For another example, my exploration/passenger ship Emerald Dawn (an Asp X) cannot equip two from this list of three modules, due to the limitations in optional slots: AMFU, repair limpets, or a cargo hold. This limits my choices to an AFMU (giving me greater freedom to "hot jump"), or a cargo hold. I also can't equip repair limpets, for that I'd need a cargo hold as well, which would require sacrificing some basic exploration equipment.
As far as I'm concerned, it's the limitations that we have to overcome that makes better gameplay. Fewer limitations results in less interesting gameplay, especially in the part of the game that doesn't have the luxury of instantaneous outfitting changes.
