I don't think Toon Link would be very pleased at all. There are a few reasons why:
1) We often see Navi portrayed as an infsufferable little sprite that needs a beating. Navi is constantly bugging you and informing you about things that we already knew. "Hey, listen!" is her trademark catch phrase, and all of us Zelda fans are sick of it. Toon Link should not have to suffer what his ancestor did - Navi should be kept away from him at all times.
2) Navi really wouldn't have much of a place in Wind Waker, would she? While fairies do exist in WW (though only in Forest Haven), there was no such speak of guardian fairies. That means that Navi no longer has any importance or meaning in he new Hyrule - perhaps the guardian fairies died out with the rest of Hyrule.
3) Navi never really had a place in OoT's story. When you look at Midna, you think "Oh, Midna's cool", but you never think "Oh, Navi's cool". If any Zelda fan ever say "Oh, Navi's cool", they must either be a) messed up in the brain or b) have absolute no common sense. Midna is cool because of her involvement in the actual story - it was her intense dethroning by Zant that made the story moodier. The fact that Zant was not the rightful ruler of the Twilight Realm, or otherwise the Usurper King, that made Midna's story so vengeful and compelling. Navi has no story to speak of, making her just another partner thrown in the game with little reason or explanation.
4) Finally, Toon Link should not have to deal with Navi because she is incredibly dull and insignificant. I honestly believe that people that played OoT never even noticed that Navi was there for the ride. Probably just another hitch-hiker.
Anyway, that's what I think about Navi - and that's why Toon Link should stamp on her with his tiny boots.