Which was an older way of saying who. So the passage is saying that Judas Thomas was also the twin, or perhaps also called the Twin.
Etymology online says, about which:
In Middle English used as a relative pronoun where Modern English would use who, as still in the Lord's Prayer.
Other English transactions leave twin in Greek, one of the languages that the Gospel of Thomas survives in. This word is didymus.
The King James Version of the Bible (original, 1611) also leaves Didymus untranslated:
Then said Thomas, which is called Didymus, unto his fellow disciples, Let us also go, that we may die with him.
(John 11:16) Notice the use of which again, where nowadays we would use who.
I think this covers the question from a language point of view, which is the scope of ELL.
For possible answers as to why Thomas was known as Didymus (twin), you could see the answers to Who was Thomas's twin on Christianity Stack Exchange.