Rules as written: No limit
Armors limit your Dex bonus to AC. Deepwardens do not have Dex bonuses to AC, they have Con bonuses to AC. The Con bonus replaces the Dex bonus (and so you would not get it in situations where you lose your Dex bonus to AC), but it still is not a Dex bonus and thus the limits of the armor do not apply. And, indeed, there’s no reason why an armor’s weight or inflexibility would prevent you from benefiting from your resilience and connection to the earth.
Intent: Unknown, and unknowable
As far as what the authors intended, that’s anyone’s guess. The author never wrote anything on the subject aside from the original publication, so we have no evidence one way or the other.
Precedent: No limit
As for precedence, generally speaking the special rules for one ability score do not apply when you swap to another ability score. There are instances where you can replace your Strength to damage with Dexterity to damage, but RAW you do not get ½Dexterity to damage on a light weapon or 1½Dexterity to damage on a weapon wielded two-handed, unless it explicitly says so. (Dragon vol. 221 has the Corsair which explicitly halves Dexterity to damage with light weapons, for example)
However, there is an FAQ entry on the question. The FAQ, it must be very clearly stated, is not errata. It is supposed to only explain the rules that already exist. If its statements contradict the actual rules, officially, the actual rules take precedence every single time. And the FAQ has been wrong many times, in many cases quite blatantly so. Finally, the FAQ is not (usually) written by the original authors of the book, so it does not correspond to the author’s intent, either.
All together, the FAQ is worth very little, and has a very poor reputation. In fact, it’s so bad that when this poster in the thread Squera linked learned that the FAQ said the Con bonus was limited, it proved to him that it actually wasn’t!
At any rate, the FAQ has this to say:
Does the deepwarden’s Stone Warden ability (RS 105) still have a maximum Dexterity bonus to his Armor Class, and does that maximum still apply to his Constitution?
The maximum Dexterity bonus should be treated as the maximum ability bonus given by the armor, so if you were playing a deepwarden wearing full plate, you would only add 1 to your Armor Class from your Constitution.
Conclusion: Rule it based on what improves your game most
Personally, I think it makes almost no sense that restrictive armor would inhibit a Con bonus to AC, I think that deepwardens make sense in heavy armor and shouldn’t be penalized for wearing it, and I don’t think the deepwarden or the AC they can get is overpowered or problematic, so I would not limit it. You may answer any or all of those questions differently. Ultimately, remember than AC is a limited thing, and lots of nasty things ignore AC; having a lot of it only does so much for you.
If you would like a compromise, here’s a suggestion. Purely houserule with no basis in the rules, either deepwarden’s or elsewhere in precedence, but it might be a good solution:
The deepwarden’s Constitution bonus to AC is limited by her armor’s maximum Dexterity bonus, just as the Dexterity bonus it replaces would be. However, the Constitution bonus is not limited for the purposes of AC against touch attacks. For example, if a deepwarden with 18 Constitution (+4) wears Chainmail (+5 AC, +2 maximum Dexterity bonus), and has no other bonuses to AC, his AC is 17 (+5 armor, +2 Consitution), but his touch AC is 14 (+4 Constitution). A deepwarden’s touch AC may not exceed her regular AC.
I don’t think this is necessary, but it does prevent the high-end AC that you might get from armor+Con, while still giving a deepwarden a good bonus for their class feature.
Remember, a class feature is supposed to make you better. Yes, Con, not limited by max Dex, is better than what the deepwarden had before, but that isn’t necessarily a problem. It’s only a problem if it’s “too much better,” and I really don’t think it is.