All perfect praise be to Allah, The Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad is His slave and Messenger.
As long as the money that you contribute to the pension plan of the company is invested in what is permissible (in islamically-acceptable activities), then there is nothing wrong with it.
The employee deserves whatever he had contributed as well as its profits when the contract is terminated. As regards the share contributed by the company, he does not deserve it unless the condition is met, and this is a type of gift contingent upon a condition. According to the view that it is permissible to make a gift contingent upon a condition – which is the view chosen by Shaykh Ibn Taymiyyah – then there is nothing wrong with it.
As for your question on how to pay zakah on your invested funds, whether your share or the share granted to you by the company, given that you take possession of it after the conditional period of time has passed, then this is considered an investment deposit, and you have to pay zakah on it as well as on the profit resulting thereof. The amount of zakah is 2.5%.
As for the time before possessing the share of the company, you are only required to pay zakah on the share that you contributed and on its profits. If it is difficult to know the amount, then you should estimate it to the point that you think that you are acquitted from your liability, and you pay the zakah on the previous years, because one is not exempted from zakah by the passing of years. You have to endeavor to estimate the sum for each year and then pay its zakah. Allah says (what means): {Allah does not charge a soul except [with that within] its capacity.} [Quran 2:286]
Allah knows best.