think it applies only at the beginning of the fight, so if the summons pop before he buffs (just like in some cases you need to toy with shield so you can have shield on clones) they might get if not i think no

It doesn't apply only on the beginning of the fight since it's not a buff that gets applied on your ninjas at the start of the battle. You'd have to test if Sakura's slugs are Konoha tagged. If yes then they are indeed protected by Chiriku's passive.

EDIT: To test this you could either compare the damage done to your slugs with and without Chiriku or get Yagura to copy someone elses Iruka to see if Iruka applies a shield to the slugs.