This is an excellent question. Generally, when a game is re-released with a slightly modified script, the newer version in generally considered "more" canon. The best example of this does actually come from GBA ALttP, where there is a change in the wording regarding Ganon's seal and the Imprisoning War; the original was worded such that, when reviewed, it could be interpreted to mean that the Seal War took place in OoT. The GBA version, however, had a slightly modified script which seemed to stray away from that idea, which was that the Imprisoning War could not occur in OoT (this is likely due to TWW, which was in development at the time). I don't remember the specifics, but Mosley wrote a great article about it a long time ago.
Usually, the changes in the script aren't substantial enough to warrant a change in the timeline; certainly not the quote you posted. The Imprisoning War quotations are the only ones that come to mind that have had a drastic impact; to some people, it is considered a "retcon" of something like a OoT-ALttP relationship (retcon being a change in overall ideas and story line that precludes a certain, previously accepted notion). However, there are a large number of people who still believe that the Seal War is in OoT, and it's not entirely unreasonable.
What has more of an impact, though, are differences in translation, usually between English and Japanese versions, that can seem to imply very different things. The most substantial one I can think of is the ending to TMC, whose last line says something fairly different in the Japanese version (you can see this in the MC thread I posted a long time ago)
As to the notion of changes in the OoT 3DS script, I think it is highly unlikely. There is very little uncertainty surrounding OoT's placement and the games around it (with the exception of ALttP), and the game is cherished by too many people for Nintendo to risk making a substantial script change. OoT 3DS will probably contain very little script changes, if any; I don't think Nintendo would take that risk, nor do I think such a risk is necessary. OoT's placement is probably the most set in stone of any game.