Translation:I do not know which tools they make it with.
Je is the accusative (one of more forms) of ono http://prirucka.ujc.cas.cz/?id=ono&dotaz=je&ascii=0
Not at all. The "n..." forms are used with prepositions. Then out of "ho, je, jej" the by far most common is "ho". The other ones are bookish and that's why I would, as BoneheadBass did, normally first think that it is in plural (them). The possibility of neuter singular comes to my only after thinking more about it.
The textbook "New Czech Step by Step" p.227 differentiates 3 types of pronoun here. What do you think of this? (1) weak/short (can only be in 2nd position): ho (2) strong/long (can be in any position, emphasizes the meaning of the pronoun): je (and "jej" I guess) (3) prepositional (follows prepositions): ně, něj