There are at least two "simple" explanations from a music theory perspective. I guess one has more to do with music tradition than music theory. A close relative of the chromatic harmonica is the chromatic concertina or "squeeze box" used to play Celtic and other types of folk music. Concertinas and other button accordions are differentiated by how many rows of buttons they have. If they have a single row of ten buttons - five on the left and five on the right, then it's common for them to be laid out EXACTLY like a 10-hole Richter tuned diatonic harmonica. If they have two rows, it's common for them to be in closely related keys like C and G, or D and A. If they have three rows, then they can play in one more key and quickly switch between them all. But some clever person figured out long ago that they could have one solo tuned row in C and another in B (!) - flat slide (!) - and they could play in any key. In other words, chromatic concertina. A popular key for Irish Traditional Music is D. Here are the fingerings for the key of D sharp slide and flat slide:
Notes: D E F# G A B C# D
Sharp Slide: -1 2 -2* 3 -3 -4 5* -5
Flat Slide: -1 (2, -2*) 3* 3 -3 (-4, 4*, 5*) -5* -5
Flat slide tuning gives you a lot more options. In particular concertina players are always looking for options that allow them to choose between an in and an out (blow and draw) to play the same note because direction changes are "expensive" and they can make some runs more difficult.
So let's say you're a chromatic concertina player who is used to B/C tuning (a.k.a. flat slide) because it makes playing in D easier than C/C# tuning (a.k.a. sharp slide), and you hear about this thing called a chromatic harmonica. You would be more naturally attracted to a flat slide chromatic.
Now, let's get a bit more music theory-ish. Consider the circle of fifths. It's enough to know that it has a "sharp side" that goes C -> G -> D -> A -> B. It also has a flat side that goes C -> F -> Bb -> Eb -> Ab -> Db. As you go around to the right (sharp side), you add a sharp for every key. As you go to the left (flat side), you add a flat for every key.
Guitar players tend to think of things in sharps because they like to play in sharp keys -> G, D, A, E. Horn players and piano players tend to think of things in flats because they "like" the flat keys -> F, Bb, Eb, Ab. Lots of big band or stage band standards are in flat keys.
If you're coming into the chromatic harmonica from a jazz band, stage band, horn, maybe even piano direction, you might be more comfortable thinking about things in terms of flats rather than sharps.
So there you go. Some fairly music theoretical reasons that someone might prefer flat-slide to shape-slide.