did you remove the pictures via the Framework Page Configuration under "Content Administration -> Portal Display" by changing the value of "Top-level navigation ->
Or did you just replace the pictures with transparent ones?
You can change the height of the TLN via the Theme Editor if you have a customized theme. Otherwise you have to copy the standard you're using and change it to your liking (because you can't edit the standard portal themes).
If you selected your theme, you find the "Outer Frame of Ajax Framework Page"-section and there the point "Top-level navigation". Here you can change the height and replace the used background images of the TLN with lower ones.
This "How To"-guide helped me ALOT: How to Customize your Ajax Framework Page with SAP NetWeaver Portal 7.30