Go to flathub and check the permission of the application that you want to install. Normally they won't have access to root directory, but could access your home dir. If they had any malicious intent, they could mess with your personal files.
I think there is another application that can restrict the permission scope on flathub itself.

Flatpak is supposed to be a sandbox, so if there is a vulnerable dependency then in theory any attack would be limited to the sandbox.

However, it depends on the software - some Flatpak need quite low level access to use, and in that case an attack or mlaware could get into the main system. And unfortunately Flatpak itself has vulnerabilities which cna negate the whole idea of a sandbox.

Flatpaks should be using up to date secure dependencies, but the reality is many do not. I would not rely on Flatpak for security. Even fully up to date Flatpaks can be insecure, and Flatpak itself have vulnerabilities that have needed fixing. And for many Flatpaks it's not even clear who is maintaining them.

Flatpaks are useful for deploying software that's just not available in your distros repos. But when deploying any software outside your repos - including App Image, build from source or 3rd party repos - you are opening your system up to security vulnerabilities. That's the nature of installing 3rd party software. Flatpak offers some reassurance compared to some methods but it's far from perfect.

If security is your prime concern, then Virtual Machines may be more secure route to sandboxing software (if done properly). Building from source would be the other option, as it means you take ont he responsibility for security by using the latest code including for dependencies. But there is no perfect option, it's always about balancing risk vs convenience.

It's also worth noting that software repos are also not perfect. But good distros invest a lot of time and effort in keeping them as up to date and secure as possible, usually via the hard work of volunteers.

I see that it can be slower because of having all the dependencies included with the flatpak itself instead of relying solely on whats installed on the system.

No. Packing its own libraries wouldn’t make it slower. If anything it would be the extra access checks added by the sandbox (which is optional FWIW, apps don’t have to use it). I haven’t ever used Flatpak but I would assume the sandbox impact is minimal if at all noticeable.

In short: No. It's getting better, but Flatpak is by no means secure. Think of it as a Windows .exe or .msi with some (not that hardened) rights management.

In addition, Flatpaks afe often community made and not even "signed" (which is not really a thing in Flatpak to begin with (yet) ((afaik))).

Something really secure would be a container, something really, really secure would be a VM, something really, really, really secure would be a separate machine. Flatpak is less secure than the least secure thing in this enumeration.

There are vulnerabilities found in Flatpak's sandboxing all the time so it's pretty much broken. The opening speed on HDD systems is really really bad too. That's why I only use Flatpak to install software that's not available in my distro's repos. Though I use Arch (btw) so distro packages being old isn't an issue for me.

It's not securely sandboxed like a Qube, but apps can have their permission to access files and such restricted. Malware can escape the sandbox, or apps may come with very permissive permissions.

I don't think speed is an issue. They're larger but all software loads dependencies from disk, flatpaks just have them bundled into a different location.

Snap did have some loading time issues but in terms of performance, I don't think there was much measurable difference.

The flatpak sandbox shouldn't be considered secure against malware. It is more of a loose sandbox.

It is technically possible for a flatpak to ship a insecure library. However, that's not unique to flatpak and I've never actually heard of that happening (I'm sure it had)

Flatpak does NOT provide sandboxing. It containerises your applications. It's better for permission management but by no means makes the system invulnerable to malware.

Quick reminder: because flatpak hides your installation state from the system, part of flatpaks could be wildly out of date or toxic releases and your system will.not.care nor even show you anything about it.

Enterprise tools - or normal stuff that acts like them - that check remotely what you have installed and let you know you're potentially out of date (like tenable but not junk) will not learn anything about flatpak content.

Good luck. Every good thing about enterprise packaging is thrown out the window. Flatpaks are toxic.