If someone cast a spell on my Master Yi with Repeat, does he have to pay Deflect cost for each repeat?

Yes — Deflect is a mandatory additional cost applied "for each time they choose me" (Rule 809.1.c), so each targeting instance costs extra.

When your opponent pays a spell's Repeat cost, the spell's instructions (including choosing targets) are executed an additional time, and those choices are made when the spell is played (Rule 820.2). So if the spell chooses Master Yi for both the initial and the repeated execution, they must pay the Deflect cost twice — and if they can't, they can't make that choice. This assumes Master Yi, Tempered at Level 6+ (the version with Deflect); Master Yi, Unstoppable can't be chosen at all at Level 16.