You cannot locate it
I'll give a concrete example: Joe fighter has been polymorphed into a mouse by the evil necromancer and pocketed to be used in a ritual sacrifice. The necromancer then dimension doors to his lab. The rest of the party, frantic trying to locate and save Joe, has the party cleric cast locate object on Joe's trusty warhammer. Being located and possibly saved would greatly benefit Joe.
But the spell says, Joe as the target of polymorph
can't […] benefit from any of its equipment
If he cannot benefit, the only logical conclusion is that locate object cannot locate the warhammer in this case.
As you can not, and as it does not make sense that locate object would work differently depending on what your intent is, the most reasonable conclusion is that locate object will not work in general, because the object is not available.
Comparison with wild shape
This is similar to the druid's wild shape ability, which uses slightly different language and says
Equipment that merges with the form has no effect until you leave the form.
Locating the equipment surely qualifies as an effect the equipment has. It has no effect, so you cannot locate it.
Now, these are magical abilities so each can be different, but treating them differently would mean that you could locate equipment merged in polymorph, but not in wild shape.