It has a pretty simple explanation.
They had no reason to believe Luffy wasn't actually using a Gomu Gomu No Mi fruit, why? Because for them the HITO HITO No MI model Nika was in possession of Shanks, which is one the reason he is so respected by the WG.
During the reverie Shanks for some odd reason went to them and said the truth, Luffy actually has the HITO HITO No MI model Nika.