I just got the blueprint for the hyperdrive. The pop up text tells me to build it in the tech section of my ship, but I read that they changed that and you have to build it in the cargo area. Is this true, should ignore the text pop up?

Either will work. You can get some percentage extra boost from the warp upgrades you'll find later if they are installed touching the hyperdrive (or another warp upgrade which is itself touching the hyperdrive, etc.), so the configuration of available slots may tend to favor one location over another.

You'll probably be trading ships later on, so if this is your first ship or it's a low-slot Class C then I wouldn't spend a lot of time micro-optimizing it.