I am not a security expert by any means but as far as I know, neither of them have had any reported issues. Cryptomator recently changed their scheme so it has been in the wild less time.
Outside of security of the data itself, both tools have their pros and cons. Cryptomator is designed to be used with local repositories that are then synced. rclone is designed to encrypt the files on the remote; though a "remote" can be local. And you can mount
or serve webdav
with it too.
Cryptomator stores the keys with the repo. I do not know if that is officially good practice or not but it is worth noting. When you change your password, it changes in the key and everything else remains. No re-encrypting.
Rclone is a bit different if you want but can act the same. With rclone, you can set the password and then if you change it, you have to re-encrypt everything. However, you can instead choose a random password(s) and then encrypt the config file. Now that config file is like your encryption key. You need to separately manage that config file and do not lose it.
rclone aims to be 1:1. You can pull a single file from the rclone remote and decrypt it. Cryptomator looks at the whole repo so you cannot manually pull a file and expect to read it. That has its pros and cons though. rclone, when encrypting the file names, makes them much longer. Cryptomator basically makes two files for every one where one has the names, etc. So you do not run into the length issue. But again, then you need the whole thing to get it back as opposed to a single file!
Performance wise, I do not know but I do know that, for better or worse, rclone offers so many toggles and flags that you should be able to tune it as you want. Cryptomator, also for better or worse, has sensible defaults but offer little in the controlling category.
While there is an app that can read rclone on iOS, it is not as sleek as cryptomator. If accessing things remotely on your iPhone (if you have one), is of concern, cryptomator is sleeker with that.
Anyway, I know I didn't directly answer your question but I hope this helps. The bottom line really is that you can use either one. Just play and see what you like more. And maybe someone has more insight into the actual security and encryption model.