I'm fairly new to the game so I did not see this first hand but, from what I heard, limpets did use to be ammo for the modules.
However, the amount was too low to be effective for things like mining.
In mining's case, you can load up 90% of your cargo with limpets and as you work it will be replaced with minerals. This makes using cargo for limpets very efficient, if a little obscure; first controller I bought, I left the station without limpets as I expected it to come with it's ammo.
A lot of things have changed since then and now we have things like SLF bays that can control 1 or 2 fighters and come with an amount of rebuilds.
I'm repeating myself from various threads but, I feel that at the very least, limpet controllers should work like SLF and SRV loadouts; the amount of different controllers is simply getting out of hand.
But for the "ammo", it's more difficult; how can we remove the dependency on cargo, while still allowing large amount of limpets? But, keeping that amount to one that make senses for the mass of the module...
Maybe limpets should be reusable, becoming a scoopable item you can pick up when the timer expires? Controllers could also have a set amount of rebuilds, like SLFs, for when they get destroyed or run out of fuel; picking up a limpet that ran out of fuel would restore 1 rebuild.