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Drop D on a 5 string

I have never had problems using thinner strings in wider nut slots

Likewise, and I've posted that a lot of times in a number of forums.

Still don't understand why poeple don't just try things themselves and if it needs to be addressed they'll know soon enough with no harm done. I't not like it's gonnas snap the neck and poke both your eyes out with the ends of shredded strings ; }
 
A little, but it depends entirely on the tone you want to achieve and the strings you normally use. They will sound different, and potentially different enough for someone else to actually care.

The real benefit to the zero fret is actually the fact that nut slot heights are nearly negligible, so it provides you with an easier means of achieving the lowest action possible.

I agree with your second point but not the first. I can't think of a single reason why an open string on a zero fretted bass should sound any different from the same note (same strings, same scale, etc.) on an identical but conventionally nutted bass.
 
HI. I have a 5 string, and don't find myself using the B string all that much except when play a song in D, and even then it is much more bothersome than just having a D string! So what i want to do is replace my low B with a D! I was wondering what gauge the D string gauge should be when using standard .045 or .050 string gauges. Also I don't want the D string flopping around, so if a set of thicker strings are needed so the D string will fit in the nut, let me know!!!

I do it all the time on my 6 string. Just tune it to D.