Im using a throwable bomb mod, but the bombs are way too big. So I used nifskope to half their size, but then the bombs in game appear outside of my characters grip and appear to float in the air.

So basically how do I centralise the newly sized mesh into their original position?

You should be able to adjust the translation values on the same node where you changed the scale. I find the game either obeys all those, or ignores them all, so If you found a place where one setting works, the others should, too.

For throwing weapons, I'm not sure where the mesh origin connects to the Biped skeleton, but the "link point" and orientation will be relative to a specific bone, most likely the hand, but it could be a finger. A sword, for example, has the mesh origin just beyond the palm of the hand, and the blade has to point the right way. A bomb probably has more leeway on orientation. The throwing knives and stars don't fit in the palm of the hand in the same way a sword does. That means the original mesh was probably offset from the origin a bit to compensate for using the same animation for a different thrown object. You may be able to invert the scaling on the translation values - i.e. double them if you halved the scale - and gt it back where it should be.

"You may be able to invert the scaling on the translation values"

What/where are the translation values? Would they be the x,y,z values? They already read 0.

Yes, I did mean the x,y,z. That would mean it's not the origin that matters, but some other point on the mesh. You'll have use trial and error on those.