Is allowing questions to be asked on a website on Shabbos against Halacha? And is answering them helping encourage Chilul Shabbos?
Similar to very common shailos where inviting a secular Jew to spend the Sabbath at your home may engender his violating various prohibitions. It is possible that even though this site operates on Shabbos, it is still OK for it to be available for secular Jews to use to draw closer to religion. A matter for a posek that is well-versed in kiruv-vs-sabbath shailos.
I heard from a Bal Teshuva that if a Jew expresses any interest in Judaism, it is a giant leap forward from the general indifference to religion that currently prevails.