Dust getting into fan bearings is usually a small consideration, although that certainly happens, and the more dust the more problems. But just as dust can do bad things to fan bearings, it is a problem for most other components inside a computer case. A dust layer impedes heat transfer; it can clog the thin passages in any heat exchanger; a build-up on fan blades can alter the fan's air flow characteristics; etc. So one is always well advised to place dust filters on the INTAKE side of the intake fans. And yes, surely that can alter the appearance of the lighting in those fan's frames.
Exactly which type of dust filter you use has an impact. The simplest ones usually are thin sheets of urethane foam (often grey), and you WILL see lights through that, although they will be somewhat dimmed and less sharply defined. Other types look more like very fine screens of metal or plastic threads, and they will interfere less with light coming through.
Dust filters work by what is called the "filtration mechanism" - surprise! As dusty air containing particles of different sizes passes though the fine holes of a clean new mesh, some are too large and "bridge" the hole in the mesh. This means that hole now is divided into two smaller openings, so it can "catch" a much smaller particle the next time. As this happens over the entire filter surface, all the openings get more and more plugged up and smaller, eventually reducing air flow through significantly. That's when you must clean off the accumulated debris and start with a freshly "clean" base mesh. Of course, the accumulated dust particles also are effective at scattering light and reducing its transmission through the dirt filter, so that's another reason for filter cleaning.