I think since the sentence mentions "endocrine cells", it makes it fairly clear that the pronoun reference is to cells. Of course this presumes that the reader knows that hormones are not cells but chemical compounds.
Consider the following hypothetical sentence:
All cricket clubs in San Jose comprise of 6 first class players, which makes them eligible clubs for "Level A" status.
Purely in terms of grammar in this case you can argue that "them" can refer to "cricket clubs" as well as "players". However since "them" is followed by eligible clubs, we know that "them" has to refer to clubs and not players.
Similarly in your sentence compare "hormones" with "players", "endocrine" with eligible and "cricket clubs" with cells.
Consider the following hypothetical sentence:
All cricket clubs in San Jose comprise of 6 first class players, which makes them eligible clubs for "Level A" status.
Purely in terms of grammar in this case you can argue that "them" can refer to "cricket clubs" as well as "players". However since "them" is followed by eligible clubs, we know that "them" has to refer to clubs and not players.
Similarly in your sentence compare "hormones" with "players", "endocrine" with eligible and "cricket clubs" with cells.
