I have been using a site to get XCI files for the switch, but what I am uncovering is that the second I go to play the game, I have to wait on a minimum 45 minute update to download.
Am I just getting it from an outdated site? Or is there a way to also get the updates needed with the XCI file?
To my understanding XCI files are direct game dumps (straight from the cartridge) - the updates come directly from the Nintendo CDN servers. Which means you "load" the game into your switch to play - it launches, dials out to the Nintendo CDN servers, sees there is an update, and asks if you want to download the update.
I asked about Freeshop for the Switch, which would allow us to get games and updates and DLC all in one, like I think you were meaning, but in order to do this you would essentially blacklist yourself and not be able to do anything online with the Switch anymore.
So the short answer to your question is No. The long answer is, if you have the knowledge and know what to search for, you can use the CDN downloader (Freeshop) to download games/updates/dlc however you will be blacklisting yourself from accessing anything online with the Switch.