Thank you for the answers, 

For first situation, we solved the problem by inserting dummy geometries to
tables which will be visible after sld apply that is at left bottom corner
of our extent which is also kind of lame but worked well =)

Secondly, I have been searching is there an option for meta tables then I
got my answer, so dummy geometry solution will persist for a while it seems.

About hinting db for using spatial index; it is not so serious issue for any
other company which is running their own databases because microsoft
published a patch to fix the bug already. On the other hand, we are using a
database as an external source and sadly we cannot force db owner to apply
the patch. 

Right now, for index issue, the solution seems using gwc as much as we can
to bypass speed issue. Unfortunately for the tables which will be changed
often, we have to find another solution.

Best regards,




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