If it is written as one sentence then you need 'all of which'. In order to use 'all of them', it would require two sentences: All of our subsidiaries try to attain this year's sales goals. Almost all of them are limited by many unexpected factors. It has to do with the function of "which" in the sentence. Here it introduces a relative clause. Consider the following: All of our subsidiaries try to attain this year's sales goals, which are limited by many unexpected factors. vs. All of our subsidiaries try to attain this year's sales goals, them are limited by many unexpected factors.