Flatpak's usefulness for programming depends on the IDE and language. IDEs like VSCode largely suck because they are not designed to work in flatpak. But some languages still do work well in them, such as Rust, since Flathub provides the Rust SDK and dependency management is done with cargo. But it sucks for C++, where you typically install dependencies using your system package manager.

IDEs like Gnome Builder are pretty good. It's designed to work within the flatpak sandbox. Even when running as a flatpak, you can choose to build things using containers or your host system. And of course also build using the Freedesktop runtimes.

I recently setup JavaFX with the flatpak version of VSCodium and have it working pretty well. You first need to install the Java SDK from Flathub, set an env variable to tell VSCode to load the SDK. The more annoying part was JavaFX since it's not part of the JDK anymore. I just downloaded the JavaFX tar, extracted to a directory called JavaFX, and set $JAVAFX_HOME to point to it. Since VSCode has host filesystem access, it can access it. Few more steps than traditional Linux, sure, but still easier than MacOS and Windows.

Not sure about your database situation though.