Any time you send it in to nintendo you run a good chance you'll get updated to 3.4 before you get it back which completely blocks and removes custom IOS', rendering your backup loader inoperable until further notice.
If you choose to use rebooter or install a mod-chip, you can remove the updates (it dummies the update partition for you) with a tool called Wiu in the downloads section in case you're paranoid you or someone else might update it, I personally rip updates from my backups just so save myself a headache eventually.
Depending on which version of 3.3u you have (there's an original release and a stealthy second one that patches more IOS') you might not even be able to install wads either if my memory serves me correct, And if you do install them I think some might not run. I could be wrong or mixed up but im pretty sure that's it.
You're always better off watching wiibrew.org about new updates and don't jump the gun, most times you'll find you could have saved yourself a lot of trouble waiting a few days instead of installing every update right away. Remember, security updates are for securing the company's interests, not yours.
Be careful, have fun and always research stuff beforehand (Like you're doing now
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