Does it hurt an adsense application if a blogger has availed first for amazon affiliate program and has an ad already in his blog while the application for adsense is still in process?
It depends. If your blog is more Amazon Associates than actual content, then AdSense would rightly reject it. If you had your Amazon links weaved into several week's worth of well written articles then it shouldn't matter at all.
what if I have placed the amazon assoc. link in my header which will appear in every post, will it matter?
No, as long as your blog is good enough in content and not against adsense TOS, then you will get approved
If you have too many ads whether amazon or any other ad program can definitely have a negative effect on your application, however if the content is good it might still get through, a lot depends on the guy who reviews you application.
i decided to take out the script for amazon affiliate ad in my site...based on your comments I think I did the right thing