Starting your maps off with a sloppy giant square skybox isn't the worst but if you become too comfortable with it you can:
- accidentally start mapping around new leaks that you will not know are there until you start optimizing the skybox placement.
- have needlessly increased compile times.
- misjudge lighting until you make a "correct" skybox.
Not to mention the crapshoot guessing Hammer does when pointing to possible leak locations.
It's a blunt answer but as previously mentioned the best way to prevent leaks is to make sure you seal your brushwork at every possible placement.
If the map is intended to be outdoor for the most part, I would say it's completely practical to cover your map in a quick skybox to prototype and such. But always consider the time it would take to create the skybox more properly on the fly, rather than having to convert a giant skybox into smaller efficient ones later, especially with possible leaks to deal with in the process.