Well, just follow the rules. First question: polymorphed into what? If it isn't a living breathing creature then we don't have to bother with this entire line of questioning.
But lets just assume we're talking about turning Zombies into a chicken because the OP doesn't really care enough about his question to provide an actual example of a case to consider.
So according to Baleful Polymorph it works like Beast Shape 3 with a target of a 1HD or less animal. Fortunately Chicken falls into this category.
Our Zombie is now Tiny, +4 dex, -2 strength, +1 natural armor, has a 10 con, and more than likely has the mental stats of a Chicken (2 int, 12 wis, 13 cha). Oh, it also has the flight and natural attacks of a chicken.
Now these are all just form changes. The Zombie remains a Zombie, so its still undead, but loses lose all extraordinary and supernatural abilities that depend on your original form, which includes undead traits. So yes you could target it with any spells that say living creature as long as it is polymorphed into a living creature. Technically you could re-animate the polymorphed zombie...which will become undone when the Polymorph Any Object runs out of duration.
If you tried a spell that specifically doesn't work on Undead it wouldn't work on the polymorphed zombie. But if you cast something that targets a 'living creature' the chicken is viable. Complicated? Yep. Just take it one step at a time and its not hard to follow.
