Hi Banda,
My experience with HP is that there are things they don't want to be
responsible for and thus, don't "support". this does not necessarily
mean that it doesn't work - just that if you have trouble you are on
your own. If I understand the configuration you are buying, you will
have a two local controller on the server for one each of two drive
arrays. The fact that the MSA 1000 has or supports dual controller is
irrelevent. That doesn't sound like a problem to me and I've set up a
few similar configurations. I use the dual controller arrays for
sharing the same array between two servers by splitting the bus on the
array.
My interpretation of the no support statement is that HPUX won't
support two controllers for a single drive array on the same server.
It doesn't look like that is what you are doing.

Take my advise at your own risk :-)