In storage, pigments and other solids tend to settle to the bottom over time. Some brands of paint are more susceptible to this than others. The longer they settle, the harder it is to reverse the process. Often, a vigorous shaking of the paint will restore it to a usable state. And yes, it is ok to shake your acrylic paints (unless the directions on the bottle tell you not to). If the lid is on tight, drying out shouldn't be a problem. I have opened bottles of Tamiya paint that are 9 years old and still usable after a good shaking.
If I am struggling with a particular bottle of paint and shaking isn't getting it done, I will use a Badger electric stirrer to mix the paint. This takes much less effort on my part, but it wastes a little paint every time I use it. Sometimes it needs to be stirred for a full five minutes to be effective. Also, the stirrer is just a little bit too big to fit into Vallejo bottles, but that can be quickly fixed by carefully grinding the mixing blade just a bit.
Preventing the settling of solids will take some work. You can store dropper bottles on their side and periodically change their orientation. This takes effort to do, of course. What I do with my Vallejo bottles is store them is a little fishing tackle box. When I am not painting for a day or two (or longer), I will turn the tackle box to one side or the other. I don't find it necessary to do with with Tamiya paints.
The solids will still settle when I do this, but with the periodic change in orientation, it keeps the solids from sitting in one place for months on end. This makes it easier to shake the paint to a good mixture when I need it.