Rather than duration, saying
He is sure that he will work for them next year as well
has the sense of it being his choice to continue working with the company because of favourable job conditions, perhaps, or the certainty that his work was well received enough that he will still have a job with this company next year. In fact, by saying "next year", this emphasizes that the company hires people on a contractual basis, where the contract lasts a year.
On the other hand,
He is sure that he will be working for them next year as well
only has the second sense of certainty that he will be rehired due to his admirable work so far.
To me, there is no question of change of duration between "will work" and "will be working" because the inclusion of "next year" makes it clear that it is precisely for the following one year.