Nope, no catch at all. You can actually download the files for games directly from your webbrowser, lmao. Tools like this just automate the download / install process and generate tickets for the games so the CFW can sign the software. It's basically just the eShop, so there's no need to worry about that. (They could restrict you, but seeing as this practice has been used for years? I doubt they will.)
When it comes to the Wii U Updates / DLC all take different file paths. So when you select a game, and there's an Update / DLC available it'll ask you if you'd like to download that as well as the title you selected. Then it'll install the game first (00050000 directory), then Update (0005000e directory), then the DLC (0005000c directory). (Only if I remembered correctly. Best thing to do is just try for yourself)
Can you explain more about what you plan to do? Because using micoSD to USB on the Wii U will NOT work. I also don't recommend using microSD to SD on your Wii U as it has its fair share of problems. Best bet is just using a regular SD.