In a low-magic game with no or limited casters in the party, the group simply cannot go on certain adventures: exploring the underwater ruins (water breathing), surviving the heat-drenched volcano rim (fire resistance), discovering the mural is actually a subtle magic portal to somewhere else (detect magic), getting 300 miles across a sea in less than a week, are all beyond their capability for some very simple examples and thus adventures/goals requiring such activities can't be introduced/followed up by the group.
In a sandbox this is less of an issue since the group can choose what they do. If the DM in that environment wants to give the group the option to go on a certain adventure the he needs to offer largesse by introducing sufficient resources to offset the low magic capability of the group -- just like you inserted the magic potions which were exactly what the group needed to continue to the next stage of the adventure.
1) he may not have humanoid minions
2) he may have humanoid minions but they can provide their own method of water breathing a la spell casting or inherent ability
3) he may have he may have humanoid minions and he provides a method to survive underwater a la aboleth, nixie, or spell casting when they visit
4) he may have humanoid minions but they don't travel to his underwater base at all because it is beyond them
So it is only "natural" if the adventure designer decides to make it natural either because it fits the initial conception or the designer recognises the need to introduce a mechanism to allow the group to proceed.
NPC allies are a form of DM largesse. The group cannot do 'X' where X requires spell casting unless the DM provides a source of 'X' -- either through item(s) or by introducing others outside the group who are willing to provide the 'X' required. Spell casting heavy groups simply do not have that dependency.