It depends on the size of honeycombing and location at which it occurred.
In compression zone like column or beam portion above central axis, it may lead to failure of component if its deep and have lot of cavities.
If it occurs in beam below the central axis (tension zone) its not a matter of much worry but need to be treated.
When honeycombing occurs, all loose aggregates should be removed and the depth of the honeycombing should be examined.
If honeycombing is gone inside the core area of column or beam, it need to be treated by adding non shrink grout along with a cement mortar prepared with aggregates of size which can fit into it.
You can also use a product like micro concrete or GP2 along with aggregates.
After repair of honeycombing, it is important to cure it properly to avoid shrinkage and cracking.
It the honeycombing or deep pocket is formed in portion such as in column top area where above slab is casted, you need to support the structure by proping it and need to grout those cavity by grouting either pressure or under gravity.
Mostly such cavities need to be repaired by grouting under gravity to ensure no small pockets left in column area.
For honeycombing which occurred in cover zone area, you can patch it up by normal mortar and do cure it or add curing compounds in it.