About Mark 16:12, I only have the TDNT at hand, which remarks (IV, 750): "The idea rests on reflection on Lk. 24:16, but is also reminiscent of popular Gk. beliefs concerning the epiphany of divine beings." Pp. 746ff offer many examples of the classical Greek or Hellenistic motif of gods appearing to humans under various forms (morphè or eidos), against which Plato polemicises with an alternate concept of the unchanging morphè of the divine (Resp. II. 380ff). I guess TLG could offer many examples of similar uses of morphè, with either allos or heteros. On the other hand, phaneroô is a Hellenistic construct and is rarely found outside Jewish or Christian writings.
As for the depiction of Thomas as "one of the Twelve" in John 20:24, it doesn't strictly imply the presence of Judas in the previous apparition: (1) it refers to Thomas status as part of a previously defined category (6:66ff), and (2) since "Thomas... one of the twelve, was not with them when Jesus came" they were obviously not twelve in this circumstance. But it is still interesting that GJohn insists that Judas' "devilish" role in the Passion plot is not an accident: Judas is deliberately chosen among the Twelve as a "devil" (6:70f). So the idea of having him remain in that group is quite appealing imo. (Whether the Judas -- Ioudas -- character is a complete anti-Jewish -- Ioudaios -- fabrication in the first place is a distinct possibility, and it would also make much sense in GJohn.)