The main differences between water based/borne and solvent based paints are -
I love solvent paints for their quick drying times, water based need a different approach in that you can't just rip off your masking or lightly sand for clearing or other layers etc. You generally need to let it air dry or use a hair dryer/heat gun to set it.
This just means you need to organise yourself a bit with your job flow.
This can be a personal preference thing, for me I find that you can get water based to spray nearly or just as good as a solvent, I've seen some awesome work done in water based paints. The main thing you will notice though (and what some people don't like about wb paints) is with water based you need to keep your ab clean/er than with solvents. Solvents are by nature self cleaning due to their chemical makeup, most spraying problems with waterbased paints are due to paint build up.
Water based paints are generally safer to use than solvent based, again due to their chemical makeup. The additives and mixing systems are usually more flexible as well. You still should where a mask with any paint regardless, this also goes for things like sanding and prepping your jobs, any airborne matter other than air is dangerous for your lungs.
Solvent based kandies are 'real' candies in that they use a dye instead of pigment. You can make a 'kandy like' paint with water based transparents by extreme extending with the base additive which some people have used with great results.
Unless you are doing some major custom work on expensive show cars and bikes etc, water based paint is a great all round paint. This is not to say that you can't use water based for these projects, some do with excellent results, it's just that most custom shops feel more comfortable using similar products for the whole job, i.e. solvent base coat, solvent artwork, solvent kandies then solvent clear. Makes sense.
Water based paint is making small inroads into this market though, it's your choice and both will work. Always do tests when mixing any paint systems though.
The reason you can use water based with solvents is that the water is just the 'carrier', once dry the piant is left which is similar to a solvent based paint. This is a very simple explanation so don't take it too seriously, but you get the idea