One use for Shatter, two for Chain Lightning
The default is to roll damage once for a spell, even if it affects multiple enemies, see Damage Rolls (PHB p. 196):
If a spell or other effect deals damage to more than one target at the same time, roll the damage once for all of them.
This is the case for Shatter, meaning that Shatter needs only one use of Channel Divinity no matter the number of creatures affected.
Chain Lightning however clearly states that (emphasis mine):
Three bolts then leap [...]
Making it clear that this does not happen at the same time so the rule for a single damage roll cited above no longer applies. However, the additional bolts happen at the same time, meaning for the secondary targets there is only one damage roll and you only need one use of Channel Divinity for multiple secondary targets.