Hi,
I actually have some worms in my Juniper, in fact I had them for a while. First make sure that they are worms and not larvae of some kind. To be honest my Juniper is young, but the worms were longer than that (more than a centimeter when spread), and they had the black line (soil). I personally like them because they air the soil and can be beneficial to drain water. But if you don't want them, or are in doubt (u don't want larvae cos it my be pest larvae) use a gentle pesticide, repot your bonsai: clean the roots (in case there are more eggs waiting)and use fresh soil.
Hope this is helpful. :)