For most day to day coding file size limits and slowness which comes from big files is not relevant. If your source files are huge you probably want to split them up more. If you have to work with big files Atom is not for you, but so are most editors. For data extraction and transformation I rather use CLI.
Where I've noticed slowdown the most is when you open up many files, I think things could be improved there, but again typically you don't need 20 files open in editor at the same time.
Multiple projects is a nice feature, but I'm already used to opening multiple windows if I do need to have multiple folders open. I'm sure the community will come up with some nice uses/plugins for it.
I think one of the biggest pluses for Atom is the active community and plugins and they're invested to keep it going and improve.