Scales are important, they are one of the most important things to practice on any instrument, but they are not magic. If you aren’t carefully listening for the right things, just playing through them won’t give you any special abilities.
There are two reasons to play scales, and each requires a different sort of practice. Fortunately, if you are clever, you can combine them.
The first reason is technique.
When you are playing a piece it is too easy to hide inconsistencies behind the natural expression of the music. Scales leave you no room to hide. They are like a control group for experimentation with your technique. Any error is made obvious.
Practicing scales without rhythm will make bad habits stronger. Always play with good rhythm. If you cannot play fast with good rhythm, then slow down!
Slowing down is a very useful technique in practicing the saxophone.
The other reason to practice scales is improvisation.
You need to learn all these different sets of notes so you can follow chord changes. This is trickier to practice; if you are playing a solo you don’t want to just be running up and down scales, but you need to know them intimately.