Upvote:1
You can visit France, or any other country in the Schengen zone, on your Canadian passport; if you enter as a Canadian and present only a Canadian passport, visitor rules will apply even if you hold citizenship of a member state. So yes, the 90 day restriction and cooling off period would apply.
For your last question, you do not have to go through non-EU exit controls if you have an EU passport, and you will not be booked for overstaying. However, it's a good idea to clear the zone on your Canadian passport rather than to have a 'glitch', however innocuous, in the computer.
Adding 19 Feb 2015 as a result of commentary
It is a fallacy to assume that the evidence used to successfully apply for Portuguese citizenship is fungible in an EU-wide context. Bestowing Portuguese citizenship is a matter arising solely under Portuguese national law and there is no reason to believe that that ancient birth records, marriage records, DNA tests and the like would be acceptable to a French border official.
They will want to see something understandable and acceptable within the EU framework. It does not necessarily have to be a passport or national ID card, but it would have to be something with a widely known (or widely recognized) counterpart in the other EU members.
And of course it goes without saying that when you are able to establish your EU nationality in an acceptable way that you can then benefit from the Free Movement Directive.
Upvote:7
The thing that's illegal is to be present within Schengen without being entitled to. Passports and entry/exit stamps are merely a means of detecting if you're guilty of that -- but ultimately what counts is what you do, not what your passport does.
Once you're a Portuguese citizen you inherently have a right to be present within the Schengen area, and therefore you cannot possibly be guilty of overstaying.
Your Canadian passport with only an entry stamp will look like it belongs to someone who has overstayed -- but you haven't actually. Once you prove your new citizenship it will be clear that you're not doing anything wrong, no matter that the usual procedure for finding out whether a passport looks suspect or not fails in your case.
You would have to provide a longer-than-usual explanation if you try to use the Canadian passport as a travel document at the Schengen borders after it has begun to look as if it is overstayed, but no actual guilt ought to attach to you.