This (January 2006) months issue of Sailing Magazine has an article detailing the method and materials required to change the acrylic lenses in hatches. The author's recommendation for sealing material is Sikaflex 295UV, Sika-cleaner 226, Sika-primer 209. He states: "There are several sealants that could be used, but I hav had the best results with Sikaflex 295-UV".
Were I to change the lenses in my hatches, I would go with the article. It is well thought out and finely detailed.
You can find the article at
http://www.sailingmagazine.net/technique0106.html