Each tool type has different strengths, with varying bonuses to mining, scanning, and damage. Personally I prefer to have two multi tools, one for exploring and one for combat. This makes it easier to cycle the modes reliably, because I only switch between 2-3 on each tool instead of 6 in a single tool.
However unless you're trying to minmax any one feature you can go with whatever tool you like. It's not going to be the end of the world to use a pistol for damage or a rifle for mining.