That hasn't been resolved just yet, but it's unlikely that George Lucas or Dave Filoni would allow such an egregious conflict of G- and T-canon to go without resolution. I'm sure we can count on seeing Slave I flying again before the series is finished. Or, if not, it'll doubtlessly be addressed by the wealth of Clone Wars novels that EU writers are almost certainly itching to write in order to rejig TCW to their liking.
At first glance that appears to be an issue of canon hierarchy. If the films or TV shows say something that contradicts the book--no matter which book--the book is what's wrong.
That said though, in this case there's certainly wiggle room. It was Jango's ship only until 22 BBY, so there's no reason to think that Boba wouldn't reconfigure the ship to his own preferences. Particularly if it took critical damage in the crash in Lethal Trackdown; that'd be the perfect in-universe reason to remodel, as well as an easy out-of-universe explanation.