May be dependant upon the instrument played. Some music is easier to read one way, some the other. But basically, simplicity wins most times. When it comes to keys C♯/D♭ for example, C♯ has 7 sharps against D♭ with 5 flats. So it could be argued that 5 is simpler than 7 to remember while reading.
With G♭/F♯, though, it's often six of one, half a dozen of the other! So brass would most likely prefer flats, while strings, maybe, sharps.
There are occasions where certain notes, though (not key signatures, note) will need to be specified. Take, in key C, G♯/A♭. It will depend on what harmony or function that note has. For example in chord C+, it has to be G♯ whereas in Fm it'll be A♭. In other circumstances, it's usual to use sharp accidentals in sharp keys, flat accidentals in flat keys. Sort of easier to keep one's mindset in one or the other. Although, frequently, I come across pieces where the chord should be spelled one way, but the dots show the other. A little confusing!
EDIT: In answer to you and which keys you should get better acquainted with - it is rather instrument orientated. With piano - all, with others, the obvious starter will be C - even if you play a transposing instrument. Then move through the circle of 5ths, both ways.
AND - by the time you are conversant with 5 or 6 of each in the key signature, you won't be concerned about another.