They weren't energy weapons...ever. Mass Effect's weapons used bars of metal. The gun shaves the metal into very small pieces, uses a Mass Effect field to reduce the mass of the object (making it easier to accelerate) then fires the mass effect field encased shaving at extremely high velocities. The metal is constructed so that it expands and flattens when it hits an object, making sure that its entire kinetic energy is transferred to the target, thereby increasing the damage of each metal flake. The ammo wasn't limitless, just every chunk of metal produced such a large quantity of ammo, a person wasn't likely to have to reload in-mission.
Just as a reference point, physics says it's possible to accelerate a paint chip to the velocity where the energy transfered is on the order of that seen in an atomic explosion. Mass Effect weapons operate on the fact that velocity is a far greater contributor to kinetic energy than the mass of the object being accelerated.
The second game just wanted to introduce clips in following with the game being more streamlined to its shooter mechanics. But to explain the appearance of clips, it describes them as ejectable heat sinks to solve the overheating problems common to the sort of guns players used in the original. According to the lore, I believe that clips were supposedly already in use in the original Mass Effect's timeline, and by Mass Effect 2 they had simply become the standard.
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