Yes, its what I recommend.
I understand with these fans an S5 will run quiet and cool. Will the stock fans run equally cool albeit louder?
Stock will likely still be cooler as its just a crazy amount of cooling. The advantage of SP120s is they are much quieter while still keeping the S5 in an acceptable temp range at most ambient temps.
So would you use 2 SP120's in a push-pull?
I currently run an s5 with 2 Noctua NF-F12 iPPC 3000rpm fans in push-pull, would the SP120s provide better performance?
That's my recommendation. NF-F12s will run cooler but will be quite a bit louder.