Why are taps kept separately from regular formulae? Why use the distinction at all?
Taps are repositories that contain formulae. All formulae, even 'regular formulae' are stored in a tap. The default tap is
mxcl/master. However, 'taps' usually refer to third-party taps.
Third-party taps contain formulae that are managed by a third-party, and therefore aren't included in the default since they can be updated at any time by the author.
Technically, there is no distinction between regular formulae and taps since regular formulae are in a tap, but that tap is pre-added.
What are the implications of installing software from taps versus regular formulae?
The formulae in taps aren't verified by Homebrew, and could contain anything. Always exercise caution and verify that the tap is from a legitimate source. In essence, core non-tap formulae are installed on a wider user base and have not only eyes from the maintainers of homebrew watching over them, but crowd sourced eyes which make compromised code less likely to be installed from formulae.