As Google was indexing your pages they saw "something" that indicates that your pages have been modified by a 3rd party.
While they have not seen anything that indicates malware, if in fact a 3rd party does have access to your site, is able to add content to your pages, they could (and probably will) add malware to your site.
In the sites(mostly wordpress) that I have looked at to date, the warning has tracked back to hidden spammy links and/or the addition of spammy pages to the site loaded with links to spammy (or other hacked) sites.
While no doubt that is going to leave most site owners with a "warm and fuzzy - the kids don't need to eat anyway" for you guys that are hard to please.
Go into your Search Console (Webmaster Tools) account and re-submit (submit) your sitemap.
Use the Fetch as Googlebot to fetch your homepage and then do a Submit URL and linked pages to index.
Go back to those search results and for any URLs that still have the hacked label and or show a spammy title/snippet -
If it is a legit URL do a Fetch as Googlebot, verify the content returned is clean, then click Submit to Index. That will trigger a re-indexing of the now clean page and hasten removal of the warning.
If it is a page added by the hackers, not a legit part of your site, use the URL Removal Tool to remove it from search results.
If the hackers have added "bogus" parameters to your URLs ?key=buy v__gra - If the parameter is NOT used legitimately on your site then go to URL parameters and tell Google to ignore the parameter.
Follow these 10 steps to ensure your website is not reported as "hacked" in Google search results.
STEP 1: Make Sure Google can Crawl Your Site
STEP 2: Determine if Your Site has been Compromised. scan it here
STEP 3: Check for a Malware Infection
STEP 4 Run the Google Safe Browsing Diagnostic.
STEP 5: Keep your CMS up to Date with Security Patches