There's nothing in US law prohibiting it. Even if there were, she could always get the current visa cancelled when the new one is issued, which is standard practice for an early renewal of a visa in the same country's passport.
There's unlikely to be any benefit, however, to an early visa application. She can -- and should -- always mention her marriage to you and your visa number when she applies for a visa, regardless of the passport she uses. It's not necessary for your applications to be submitted together, and it's certainly not the case fat they would disregard your marriage because you present yourselves with different nationalities: there are many couples who do not share nationality.
If she waits for her current visa to expire, she can apply using either passport for the subsequent visa. In fact, she's probably more likely to receive extra scrutiny if she applies for the next visa using the current passport before the current one expires. The extra scrutiny probably won't go beyond "why are you applying now when you already have a valid visa?", but you never know.
Further information: the US Foreign Affairs Manual permits consular officers to issue concurrent visas in a dual national's passports only if the visas are of a different type. See https://fam.state.gov/FAM/09FAM/09FAM040309.html:
d. (U) Dual Nationals: A dual (or multiple) national who possesses a passport for each country of nationality is permitted to have a visa issued in each passport, provided the visas are of different classification.
Therefore, if your wife applies for a new B visa before her current B visa expires, the old visa should be cancelled, regardless of which passport she uses.