Splitting those functions into different libraries was indeed done to differentiate which ones were able to be run on a Windows host system. For example, you can use "RT Ping Controllers.vi" on both a Windows host and an RT target to find other RT targets, but the "RT LEDs.vi" can only be run on an RT target and wouldn't work on Windows. The reason this was done in LabVIEW 8.0 is that with the addition of the project, the palettes are now context sensitive. That means that the palette will change based on what type of target the VI is opened under. (You can quickly see the target a VI is opened under in the lower left corner of the VI.) If you look bring up the palettes on a VI under an RT target you'll notice that the controls palette for example doesn't have the ActiveX container in the Containers sub-palette because it isn't supported. Not only are we now able to customize the palettes for Windows versus RT, but we can also customize based on the type of RT target. For example the "Real-Time Watchdog" palette should show up for all NI RT targets such as PXI and FieldPoint, but it doesn't show up for RT Desktop targets since they don't have the custom hardware interfaces required.
So you shouldn't have to worry about the internals of where the palettes are pulling VIs from, but that is the reason why.
-JR A.