I have submitted simple text sitemap to Google Webmaster tools and after few days it was crawled, after few more most links were indexed according to GWT but it is not showing those links in google. If I do this search (site:domain.com) I only get few url's instead of a few hundred. Is there a delay between GWT showing that pages are indexed and those pages showing up in search results?
Google may crawl your page, and show it in GWT, but still not bother showing your pages on the SERP page.
This will, for instance, happen if Google think that your site is without interesting or original content, or if Google think you're doing black-hat SEO.