Geoff is right about 6.3 not being compatible with CS4. Nikon D5000 is compatible with ACR 5.4 with Photoshop CS4. The 6.3 update is only to add two more of the Nikon camera range for CS5 - the D3100 and D7000 See list here:
http://blog.gerardprins.com/pdf/Niko...ibility_en.pdf
Updates are generally to add new camera support to the list and seldom have any other benefits. It's best to always check with Adobe before updating anything.