Official guide says:
"The Ti.UI.FILL behavior represents growing a view to fill its parent's dimensions. Note that the FILL behavior doesn't take into consideration other sibling elements in the parent."
http://docs.appcelerator.com/platform/latest/#!/guide/Layouts,_Positioning,_and_the_View_Hierarchy
For sure Ti.UI.FILL is a Titanium constant you can use everywhere as is, while 100% is a string. I always prefer the first one.
There could be a difference when we put two elements in the same container giving to one FILL and the other one a fixed size, or giving 100% to the first one and a fixed size to the other one, but usually when I use a view which should fill a space it's the only one in the container so I've never noticed any difference.