1. What do you recommend I do about disk partitions?

The basic is /home split from / that way you don't lose your data should you need to reinstall.

I'm keeping a Windows install for the few things that demand it, does Windows still occasionally destroy Linux partitions?

Not asuch as before, but I think it still sometimes it does. I think the recommendation is to use UEFI and have a /boot sp ok it from the Windows EFI one, but I haven't used Windows in a long time so better check this

Do I need separate partitions for data and OS?

You don't need to, but it's better for you if you do, since that allows you to not lose data should you want to switch distros or reinstall the system.

Is it straightforward to add additional distros as new partitions or is that asking for trouble?

Only time I tried that (many years ago) I fucked up everything, but in theory it should be doable.

2. Is disk encryption straightforward? And is that likely to upset the Windows partition?

It's straightforward (a checkbox on most distros installer) and Windows won't care about it.

3. Is cloud storage sync straightforward? It's my off-site backup solution on Android and Windows (using Cryptomator with Dropbox, Google Drive, etc) but I don't think that many providers have Linux clients. Is something like rclone recommended?

Drive doesn't provide Linux client, Dropbox does. Like you mentioned there are other tools, such as rclone, for accessing drive if you want to.

4. Should I just use apt to install software? I know there's some kind of graphical package manager (synaptic?), does that use apt under the covers or is it separate? Is it recommended to install something like Flathub too?

The GUI (like usually on Linux) just uses the CLI tools, so yeah, the graphical package manager just uses apt under the hood. However it also uses snap/flathub as well. Should you care about those? Maybe, some software is only available there because the devs don't want to maintain multiple distro packages. But I wouldn't use snap/flathub as my default (especially not at the beginning) even if they are theoretically more secure (especially because they are more secure, meaning they need control access to other stuff, e.g. zoom unable to detect you have a camera, or Firefox not able to download things to the download folder because of bad permission configurations)

5. Any other pearls of wisdom? How do I keep everything tidy? Any warnings about what not to do? Should I use a particular terminal emulator or Firefox fork?

Just a note on hardware compatibility, some cards are not very compatible. If you like to game (you did mention a steam deck) and you have an Nvidia you MUST use the proprietary driver. However the proprietary driver SUCKS on Wayland, so you're stuck on X11 for the time being.

Besides that some wireless cards are not properly recognized, you will realize this quickly when you boot the live iso if that's your case.

Finally I would recommend Mint instead of Ubuntu, they're still on X11 and are not forcing Snaps down everyone's throats.