Not by default, but it makes it a lot harder. It sounds like you need encryption at rest minimally, but even then you need a way to exchange encryption keys. If someone has physical access to the device that might be accessed regardless of your solution.
There’s a few topics out there discussing this situation, you might find more tips there. Which I see you’ve posted to already. And remember, even if you had compiled binaries, if they can be accessed chances are they can be reverse engineered with effort, expensive tools (e.g. ida pro) and time/motivation. Or interacted with through injection of code into the process, for example with Frida. Can you explain more about your use case that makes it so sensitive that your flows have to be deleted? Is it just trade secrets for competitors, or are you working in a specific sector where everything is sensitive? And think about this: it might have taken you months to create this prototyping specifically for a raspberry pi and node-red, but if the keeping it out of other people’s hands part is so important, is node-red/raspberry pi the best combination for your situation? Do a risk assessment, and figure out if the (financial) impact is worse than having to restart with what you’ve learned so far, on a platform that gives you that better protection.
PoC||GTFO is one of my favoured pastime readings. If there’s one thing I’ve learned from it as that as long as people have motivation, very few physical devices can withstand the reverse engineering efforts.