Yes, but there were native independence movements, they just were based elsewhere.
People born and bought up in Cabo Verde were high up in either the active resistance movement in Guinea-Bissau or the party in exile in Guinea-Conkary. Likewise people born and bought up in Sao Tome had established a resistance movement from Gabon.
The post colonial leaders didn't come from nowhere, they mostly just returned from exile. Like by 1972, the African Union had already recognised native governments based elsewhere in Africa as the legitimate of rulers of Cabo Verde and Sao Tome.
I don't disagree that a more right wing government could have held onto both areas but the idea that this was a decision made purely based on the situation in Portugal rather than the one in Africa isn't the entire story. This isn't an Azores or Maderia like situation where there was no serious support for independence at all until the Carnation Revolution after which rebels suddenly started to emerge, they already existed.
Also given that there were bombing campaigns by separatists in both the Azores and Maderia in the mid 1970s without any previous resistance infrastructure means there's definitely going to be some in both Cape Verde and São Tomé.