Is it a good decision to use Lucene over free text search in MS SQL
server ?
It depends on the amount of data and the query flexibility you want. If you have a large amount of data and you want very flexible queries, yes it is.
What are the implecations that I need to take care?
You will need to manually keep your lucene indexes up to date with the database, and you will need to handle the free text search yourself.
Is it possible to use MS SQL Sever to store indexed documents in
Lucene over file system ?
see http://wiki.apache.org/lucene-java/LuceneFAQ#Can_I_store_the_Lucene_index_in_a_relational_database.3F
I'd recommend you to take a look at the Lucene java FAQ, pretty much everything there applies to Lucene.NET as well and it adresses lots of other questions you may have.