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
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.