Yes there are disadvantages, first of all you cant see the turbine, and will have no idea that you had a wet start as I discovered on a AW L39 with burnt bearers and also on some installations you can in fact reduce the volume of air the turbine needs to suck especially on larger turbines fitted in smaller models which is fairly common with guys over powering a model.

I read somewhere Jet Central stating it was not advisable to use a bypass on their larger turbines.

I don't really feel there is any advantage, it may be slightly more efficient on fuel (minimal) as the turbine dos'nt have to suck a hard with the ram air effect but that could actually cause a problem if you were going flat out then shut the throttle quickly as the ram air tried to turn the compressor faster than it wanted to go.

My feeling is there are far more disadvantages than advantages, the bottom half could be useful to help prevent stuff getting sucked in through gear doors etc, but a piece of ply or lite alum from a drinks can, will also do that.

What you have to remember is it is not in fact needed or required at all for any reason.