Those spaces are reserved for some features you may not have installed.
For the first image, you've got to have a space somewhere. If it isn't there, it's going to be somewhere else on the pattern of 6. On my installation, the empty spot has the Adaptive Filters palette located there. But I also have 10 other buttons for palettes above what you show related to waveforms and filters.
For the second image, it does seem like a lot of unnecessary space. But I don't have teststand to be able to see that palette or to know what other items could possible belong in there.
a) Moving items in the palettes around is frustrating to the muscle memory that users develop, so when we have toolkits that install additional functions, we reserve space for them so that adding the toolkits does not move existing items.
b) Similarly, sometimes we leave blank space in case we add additional functions in future versions of LV.
c) Sometimes we leave blank spaces to isolate chunks of functionality because the separation makes it easier for some users to spot the items they are hunting. The space may not be helpful to all users, yourself included.
Pretty much every space you see is deliberately placed there. They don't happen by accident.
Declined for reasons listed here: http://forums.ni.com/t5/LabVIEW-Idea-Exchange/Unnecessary-spaces-in-the-palettes/idc-p/3268994#M3464...