In the The Incredibles, when EDNA takes in Elastigirl to show the suits details, the guns pop up.
But in Incredibles 2, when she takes in Bob and Jack-Jack, the guns do not show up.
The suit is bulletproof, as a default, there is no need to prove it over again.
Edna..in The Incredibles
Edna: Shh! Darling! Shh! I cut it a little roomy for the free movement. The fabric is comfortable for sensitive skin, and can also withstand a temperature of over 1000 degrees. Completely bulletproof. And machine washable, darling. That's a new feature.
What on earth do you think the baby will be doing?!
Well, I'm sure I don't know, darling. Luck favors the prepared. I didn't know the baby's powers, so I covered the basics.
It occurs to me that you might be referring to these guns...
However, we don't see the entire clip (I'm dubious about the legality of the youtube clip, but that's another matter)...but it seems likely that since the reason for the visit is to authorise Jack-Jack to the testing area the guns aren't necessary....assuming they deployed in the first place (since we don't see them). Edna's already approved him and the machines are just recording the details.
Plus, of course, he's already wearing his bulletproof onesie!