Yes and no. Isobel knows Clark has super-powers, but she assumed that he
was a warlock using magic.
She seemed to have no clue that he was an alien.
It's hard to say. Isabelle apparently knew all about the magic stones,
and hunted for them for 400 or 500 years (or whatever). It's certainly
plausible that she knew about Krypotonians. I assume she could read the
language.
She obviously had some link to Krypoton.. otherwise, why would a
Krypotonian symbol be on her backside and all over her spell book.
Logically, yes, Isabelle should've guessed that Clark was Kryptonian.
However, this is Smallvile, and it wasn't convienent for her to know.
The whole Isabelle story was handled poorly, IMO. She could've been a
great adversary for Clark if they gave her intelligence. But the
writers made the whole Isabelle character inconsistent.. For example,
as soon as she saw Clark in China, why didn't she cast the spell that
removed his powers? Why did they even give Isabelle that incredible
power and then have her forget that she could do it? Lame writing.