It's not that deep. She's just frustrated that they were unable to do anything against Gunko which is fine, even Jinbe was powerless against her so Nami's strength isn't the issue here. Most of the time when faced with these kinda of monstrous opponents, the M3 are usually strong enough to take care of it in some capacity so don't think it's necessarily wrong for her to have expected more from an ex-Shichibukai in Jinbe. If anything this isn't as much of a slight on Jinbe as it is hype for the Holy Knights and potential gas for the M3 who will most likely perform better against them.