As mentioned by kassak, this issue is down to the window manager and the individual applications. There's not much we can do for the application outside of getting the source code and modifying them to work at smaller sizes.
We can deal with the window manager though, what you need is either a tiling window manager, or one that can control the DPI or scaling. I have no experience with the former, but for the latter I recommend xfce4, it's very light weight, so the Pi will handle it fine, and it has a settings manager window which wraps around all of the various settings editors, this means that if the setting you want is off screen you can scroll to access it, even if the developer set a fixed window size.
Instructions for how to install xfce4 can be found quite easily, but I won't link so the links don't go stale.
To change the DPI/scaling will depend on the window manager you choose. For xfce4 go:
- Applications menu (should be top left by default)
- Settings Editor
- Fonts Tab
- Tick "Custom DPI Setting"
- Change the number to the right to what feels best to you