Yes you can. You can go to the mod folder, And make a Folder with a mod name of your choice eg."Music mod"
And in that folder you make another folder called "Sound" .
(The mod folder is MyDocuments/Appdata/Local/Ironclad Games/Sins of a solar empire/Mod-Entrenchment v1.401)
Now you just put bunch of Music you like in .ogg folder and name each one the same as the original sins music names Such as
Battle 1
Vasari Theme .....etc
When you go into the game, all you gotta do is enable this little mod you made, And its 0 checksum so you can play with it online too.
I play with my custom musics all the time.