Just theorising based off things;
"They were not truly living, but instead suits of armor controlled by the leech-like Kraata of their original form."
As such while the Kraata may have gender, the suits (Rahkshi) would likely not.
Given there are multiple different breeds of Kraata, chances are they intermingled as such I'd say they probably would have a gender.
"The Bohrok were a race of hive-minded, mechanical insectoid creatures, controlled by strange, parasitic creatures within their heads known as Krana."
As such the Bohrok appear to have been a race before being controlled by the Krana, so in this case the Bohrok should have genders.
The Krana I'm unsure about due to the nature of them as a parasite
"The Vahki were designed by Nuparu to help keep the peace in Metru Nui, and were produced en masse by the city's Po-Matoran. It is believed that there were 5,000 Vahki created."
As such I would go under the belief that they have no gender, simply being robots.
Given they are a species, despite being one that was created, they probably have genders for the purposes of reproduction and growing the scale of the army.