There are physical conditions unique to men that are disqualifying, just as there are ones that only apply to women, for purely anatomical reasons, not misogynistic ones in the case of women.
The rationale behind the list of DQ conditions is, to put it very simply, is that military life demands, at the service intake point, people who are in the best health possible, with very little "broken" about them, so as not to endanger the person or those with whom they are serving in an area with limited or no advanced medical support. The needs of the service will come first. That means minimizing the chances of impact on unit readiness and end strength for health reasons.
Some of the underlying conditions causing amenorrhea can be quite serious. Sometimes it is a temporary condition related to heavy training and decreased body fat. The starting point is a DQ.
Being DQ does not automatically equal "not a chance." If the condition has been diagnosed, and medical records showed favorable response to treatment and eventual resolution, then the door to the remedial and waiver process MIGHT be opened. DODMERB DQs. The services MAY waive, depending on their particular requirements.
There are several threads on here about that process, for various conditions.
