Yes varnishes do protect your models, the formula contains acrylic polymer suspended in water which evaporates when you brush/spray onto your model, leaving a continuous film of clear acrylic which is somewhat resistant to oil/grease, water, scuffing, marring, scratches etc.
Almost all acrylic emulsions are glossy by nature, and so glossy varnishes can usually contain a higher % of acrylic but I don't think this is the most important factor. Not all acrylic emulsions are created equal, and there are a vast range available from many big and small chemical companies which will offer different properties of interest to us hobbyists.
The Vallejo matte varnish at least claims to be 100% acrylic resin, and I think this may indeed be possible as there are a few acrylic emulsion products out there that are innately matte in finish due to the controlled polymer particle size. Most matte varnishes and paints contain a matting agent such as fumed silica which controls the level of gloss, but in my experience it has no effect on the durability of the final film.
It is also not only the acrylic resin which provides protection on your models. Every decent paint and varnish will contain a small amount of silicone additive which gives "slip," this is what makes it harder to scratch the paint or varnish off.