I have the same machine and so far ( 3+ years) haven't had trouble with any threads. I mostly use Aurifil but have used many others. One very low lint is Isacord that I use for machine quilting mostly.
As for cleaning, I don't know Janome but I don't find my Bernina hard to clean out. I oil it a lot and don't have a lot of buildup because of that.
I must say it's my very favorite machine and I find I don't want to sew on any of my others anymore.