I imagine that--since woman is not (or, at least, shouldn't be) defined by genitalia--whatever the physical state of their bodies before reincarnation is the condition of their bodies after reincarnation. Which means, some trans Amazons will have penises and some trans Amazons will have vaginas. Or some may be intersex and have both.
I make this deduction because trans men--whether they have vaginas or penises or whatever else--will not be reincarnated on Themyscira. Meaning that what's pertinent is not the physical state of the body but the gender/identity state of the body, heart, mind, and spirit.