Not sure but I think your SERPs will be affected. I suggest you remove all the malicious code etc from your site and then request a re inclusion request in google webmaster tools.
I had the same problem but once fixed this issue google removed warnings within one day time. Only few of the pages showing warning that also will be removed soon. It doesn't affect any SERP for my website.
Just to clarify a re-inclusion request wouldn't make any difference because my site hasn't been removed from google, It has merely been dropped in the search engine rankings. I am up to 80 visitors a day now on this site, next to nothing
Reinclusion request will definitely make a difference. One of my sites was hacked in May and had a similar problem. I corrected the problem and filed for reinclusion. My site was reincluded, but the hacker again hacked it. The site was again penalized (See the spike in June. Traffic was normal only for a day). Once more, I corrected the issue (This time I took some additional precautions..). I again filed for reinclusion and my site was again reincluded. Both times the penalty was removed 2 weeks after the request and traffic returned to normal 3 weeks after the request.
Just wonder why people don't want to try and follow the steps suggested by Google, given that the steps are easy and don't cost them anything? It looks like the problem is not that serious for them.
Google should not put the onus on people to contact them for reinclusion, they should be going through their penalized site list and unpenalizing them themselves so many webmasters are being unfairly punished by google
Re-inclusion isn't part of the steps suggested by google after a malicious attack on your website. It seems however that my traffic is slowly increasing again, hit the 100 mark yesterday
serious sites should care about security, so it's normal if google penalizes hacked sites if your site is hacked, part of it it's your fault
I am agreed that Reinclusion request will definitely help. I also did this last year in December 2007 and successfully get the results