According to Trinitarian theology of Calvinism, was the Word (2nd person of the Trinity) missing from heaven when He (the Word) incarnated on Earth? What I mean with "missing from heaven" is something like this : 
A. Only the first and the third persons of the Trinity were in heaven because the second person was on Earth.

Example:
Q : Where is the second person of the Trinity from 1 AD to 33 AD ?
A : On Earth in the flesh.
Therefore there is no second person of the Trinity in heaven.



Not "missing from heaven" is then something like this: 
B. The first, second and third persons of the Trinity are still in heaven although the second person is at the same time on Earth.

Example:
Q : Where is the second person of the Trinity from 1 AD to 33 AD ?
A : On Earth in the flesh and in heaven just in spirit.



So, according to Trinitarian theology of Calvinism, was the Word (2nd person of the Trinity) missing from heaven when He (the Word) incarnated on Earth (John 1:14) or was He in heaven at the same time as He was on Earth?

Thank you.
Ah, the extra calvinisticum as it was derisively called by the Lutheran Reformers. The Reformed position is that although the Word is fully united to the human nature it could not completely contained by it. 

The Belgic Confession discusses the two natures:


  We believe that by being thus conceived the person of the Son has been inseparably united and joined together with human nature, in such a way that there are not two Sons of God, nor two persons, but two natures united in a single person, with each nature retaining its own distinct properties. Thus his divine nature has always remained uncreated, without beginning of days or end of life, filling heaven and earth. His human nature has not lost its properties but continues to have those of a creature-- it has a beginning of days; it is of a finite nature and retains all that belongs to a real body. And even though he, by his resurrection, gave it immortality, that nonetheless did not change the reality of his human nature; for our salvation and resurrection depend also on the reality of his body.


The Divine nature was always filling heaven and earth. Note that this continues today with the locations reversed.

From the Heidelberg Catechism:


  Question 47 :Is not Christ then with us even to the end of the world, as he has promised?
  
  Answer: Christ is very man and very God; with respect to his human nature, he is no more on earth; but with respect to his Godhead, majesty, grace and spirit, he is at no time absent from us. 
  
  Question 48: But if his human nature is not present, wherever his Godhead is, are not then these two natures in Christ separated from one another?
  
  Answer: Not as all, for since the Godhead is illimitable and omnipresent, it must necessarily follow that the same is beyond the limits of the human nature he assumed, and yet is nevertheless in this human nature, and remains personally united to it.


So, the Godhead is 'beyond the limits of the human nature' and 'omnipresent'. Today, while Christ's body has ascended to Heaven, his Godhead is still with us -- beyond the limitations of the body. Likewise, while he sojourned on earth, His Godhead was still (also) with the Father and Spirit.

Answer B

It should be noted that this idea is often identified with Calvin, it can be found in the Fathers as well.