The good (and sometimes not so good) aspect of Migration Assistant is that it does a remarkably good job of reproducing what you had before. You will see once in a while some posting in these Discussions about Migration Assistant not working, but for me, using a Time Machine (and once a bootable "clone") backup external drive, I have had very smooth migrations in the ~ 15 or so times I have used it, usually when moving to a new machine, once when needing to do a "clean install" due to a hung Security Update.
Now for your issue: if you do a clean install of the MacOS, presumably you mean erase/reformat and reinstall of the MacOS, but then follow with Migration Assistant to restore all your files, installed software, plug ins, etc. ... you will end up with a very exact reproduction of what you started with. So that would likely include the trouble you had with your apps.
There are two possible causes for your troubles with the software. Once is a corrupted part of the MacOS itself. This is MUCH less likely than it used to be before Catalina. The reason being that Catalina keeps the MacOS in a protected hidden virtual disk that apps (and users) cannot tamper with. While it is always possible that a cosmic ray or other electrical glitch flipped a bit and damaged the MacOS ... much more likely is that there is a corrupted file (preference, setting, etc.) somewhere associated with those third party softwares, as those files get written to and read from frequently. Or that the software has bugs or is not 100% compatible with Catalina. These latter things are common. Some bugs are as simple as mishandling memory, such as memory leaks, which can cause freezes, crashes and the like.
One solution is to clean install, use Migration Assistant to only migrate over user accounts and files, but no settings and no applications. Then applications must be reinstalled from scratch. Since user files were brought over, this MIGHT get rid of the damaged preference file or settings file.
You said you don't want to reinstall applications from scratch. But then you will have what you had before. It's a quandary. I have personally done the reinstall of all third party applications and it resulted in a much snappier machine with no freezes since then (2 years since, for an older laptop on High Sierra). This would not entail recreation of libraries and data files, those would be brought over, but the applications themselves would have to be reinstalled and set up again. You have to balance the time lost due to glitches and crashes, versus the time spent to reinstall all applications from scratch.
