Well, if you're concerned then just try a little matte medium thinned with some clean water.
You can also use Citadel's Lahmian Medium, or their Contrast Mixing Medium, or Army Painter's Wash Medium.
All these are is essentially "blank" paint - i.e., no pigment. So they are transparent, especially when applied thinly, and have a nice matte finish.
They don't offer any protection like varnish if course, but they are useful for unifying different finishes, and are "supposed" to be mixed into washes and paints to make them more translucent.
If painting over decals causes them no harm, then the medium will also be fine!
