This is especially evident in the "Half-Vulcan Science Officer" bit, because Mendez had just uttered that phrase as a casual, rhetorical way to emphasize that Kirk's Spock was the very same Spock mentioned in the report. And then the document absurdly prints out that highly informal and personal verbiage. It was a private joke.
I don't think it was meant as a joke. The phrase "half-Vulcan science officer" wouldn't have sounded as forced or strange to the producers in 1966 as it sounds to us today. Vulcan wasn't even established as a Federation member until "Errand of Mercy" -- and the Federation wasn't even mentioned for the first time until "Arena." The text of the file Mendez reads from refers to the
Enterprise as an "Earthship," not a Federation vessel. So if they were still assuming that the E was an Earth/human vessel, then the fact that its science officer was half-alien would've been seen as anomalous enough to be worthy of comment. Particularly since, at the time, Spock was the only nonhuman Starfleet officer who had yet been seen in the series. So no, it wasn't meant as a joke, because it didn't look the same way to them that it looks to us decades later, when we take the nonhuman members of Starfleet for granted.