I wonder when we use "mi" and when when we use "midir" in a question.

We use "mi" in a question where emphasis is on an adjective. For example: Hayat kısa mı? 

In the question where emphasis is on a noun, we use "midir".

Ex: Bu senin kalemin midir? or "Bu kalem midir?"

Am I thinking right? If not, I´d very appriciate if you guys can help me correct it!

I never used midir in my life. :O

As I see, you´re native speaker, aren´t you? So why don´t you use midir, Abla? Is that because mi can be used instead of midir in all cases? For example: Bu kalem mi? istead of Bu kalem midir?

Abla is not a native speaker. But I am. Using midir, you can ask your question in a formal way. But most of the time we dont prefer using -dir suffix. Becuase using it everywhere sounds so unnatural. You should know when or where to use it. 

Like the above commenter said, I think the suffix "dir" (and variations) is just a formal/emphatic way of putting things. Here is a quote from turkishlanguage.co.uk:

Present Tense only:

(This not does not apply to the past tense below)
Third Person Plural ending shown in brackets above are very often omitted in conversation. They are added only for emphasis and for public advice, notices and warnings. They are also used when stating an actual fact. [Apples are fruit - Elma meyvedir]

I don´t think it´s that simple. As a native I can use it in any way without any problem whatsoever but it´s hard for me to describe perfectly in such a perfect way that non-native speakers can understand it perfectly.

First of all it´s an overloaded suffix. Sometimes you can use it for probability (for example when you are speaking about something that you are not sure of) and sometimes for info passing (if you have a feeling that you are giving -or passing- some information to the addressee that you think he/she is not aware of), etc.

Sometimes you feel like the meaning doesn´t change much (or at all) when you omit it but sometimes you sense some difference in meaning when you omit it (and it´s hard to describe here, sorry).

How can you express probability or pass information in a question?

Acaba gelmiş midir?

Edit:

"Acaba gelmiş mi?" would be a question not expecting an answer from somebody you talk to.

"Acaba gelmiş midir?" would be a question expecting an answer from somebody you talk to. So you request from him/her to pass some info (his/her opinion maybe)?

I see.

"Overloaded suffix" is a good description for DIR I guess. DIR kind of opens the door for various modal meanings concerning the truth value of the proposition and the speaker´s attitudes towards it. Göksel and Kerslake call it the marker of general modality if my memory does not fail me.