Polymorph et al. are broken and should probably be banned at just about every table
The far more reasonable spells of the Transmutation (Polymorph) subschool, as seen in Spell Compendium, Player’s Handbook II, and elsewhere, are a much better solution. For that matter, back-porting the changes to polymorph effects from Pathfinder is also a better idea than using those spells as-is in 3.5.
And if you need more reasons why than as posted in the “How is Polymorph ‘broken’?” question, consider the Polymorph subschool itself, including an actual mea culpa by Wizards of the Coast that confirms that they themselves have come to realize the spells are broken. Even Paizo, which ignored a lot of problems in 3.5 for Pathfinder, saw this problem and actually put effort into fixing it. Everyone can see that these spells just need to die.
If you insist...
You have to check on a case-by-case basis; there is no one rule governing all such creatures. You certainly can change into them, and would at the very least have the appearance of the extra heads, but whether or not they do anything for you depends on the form of polymorphing that you use and the type of ability that confers benefits based on multiple heads.
For example, polymorph gives you extraordinary special attacks, but not extraordinary special qualities, and does not grant any supernatural qualities or abilities at all. Alter self also lacks supernatural abilities, but gets all forms of extraordinary abilities (attacks and qualities) except those that “any extraordinary special attacks or special qualities not noted above under physical qualities,” but what that means is incredibly ill-defined. Shapechange gets supernatural abilities. Alternate Form and Change Shape each get a fairly specific selection of abilities that go across the types of abilities.
But the real problem is abilities that don’t specify a type. In one of the most blatant cases of broken rules regarding polymorph, abilities that do not have a specified type? Those are “natural abilities,” which are a barely-mentioned, poorly-defined “other” category. They are part of the physical form of the creature: as such, they are something you get when you have that physical form, as with polymorph, or even alter self for that matter. In effect, if you actually have the form (i.e. it’s not illusory), you get these.
Unfortunately, most monster designers don’t seem to have known that. Some ridiculously crazy things don’t specify their type. This appears to be intended as a “none of the above” rather than defaulting to natural, but who knows.
Hydras are a great example. Almost everything they get, is described in the Combat section, with no type specified for the abilities. Thus, you get the Hydra’s many heads, their head-regrowing abilities, their ability to attack independently, and even the breath weapons of cryo- and pyrohydras, since unlike every dragon in existence, those are not specified as supernatural, or indeed as anything at all, which defaults them to natural abilities. So polymorph gets that. So does any other true transformation. Polymorph misses the Darkvision, Fast Healing, Low-light Vision, and Scent, but those are relatively minor and many other forms of polymorphing do get them.
But you want something even more absurd? Most creatures’ natural spellcasting abilities are not specified as a special attack or quality, do not have any Ex, Su, or Sp tags, and thus default to natural. That means you can polymorph into creatures to get, oh, the spellcasting of a 20th-level cleric (Solar).
And while these are obvious cases of absurdly broken things that you can easily houserule, tons of creatures are going to have to be determined on a case-by-case basis. You do not want this headache.
I'm tempted to rule that you cannot polymorph into creatures with multiple heads like Ettins, Chimeras, Hydras, etc. Because the multiple brains require multiple minds/personalities/entities. Is that OK?
Your “because” is not actually true, or at least not stated to be true in the rulebooks, for most multi-headed creatures. Ettins are kind of famous for it, and the fluff behind their Superior Two-Weapon Fighting requires having two minds that have independent control (though polymorph wouldn’t get that because it is a Special Quality, so that kind of works out), but most creatures don’t really even imply things one way or the other. So that because is only true if, ya know, your setting says it is, which is probably a DM call every time.
Moreover, that spells would be incapable of accomplishing that is also unclear. Polymorph, probably couldn’t, but shapechange is an absurdly powerful spell, being 9th-level and all. We already know it can do things that are easily as ridiculous.
But does that means it’s “not OK”? You’re talking about nerfing polymorph effects, that is almost always OK, or actually it’s not OK because it’s not enough: they should be banned and replaced with limited, specific effects.