Yes, this works.
There is nothing in the feature description that says otherwise, so you may do this. The Replicate Magic Item feature reads (E:RftLW, pg. 63):
You can learn this infusion multiple times; each time you do so, choose a magic item that you can make with it, picking from the Replicable Items tables below.
Each time you learn the infusion, you choose a magic item from the table; no restriction is given for choosing an item you have chosen before.
Note, a single character would not be able to benefit from two of the same passive-effect magic item, such as two rings of protection. The DMG has a rule, Combining Game Effects:
Different game features can affect a target at the same time. But when two or more game features have the same name, only the effects of one of them—the most potent one—apply while the durations of the effects overlap. [...] Game features include spells, class features, feats, racial traits, monster abilities, and magic items.
Since a bag of holding is just an item, not an effect, there is no reason you could not create two of them using two of your artificer infusions.
It may be worth addressing this phrase from the feature description of Artificer infusions:
You must touch each of the objects, and each of your infusions can be in only one object at a time.
It should be obvious that this does not restrict using the Replicate Magic Item infusion twice, as the rules would not let you learn the infusion twice if you could not use it twice.
This is definitely rules as intended.
The Unearthed Arcana version of the Artificer’s Replicate Magic Item ability reads:
You can learn this infusion multiple times; each time you do so, choose a different magic item that you can make with it...
The word “different” was deleted for the official release of the Artificer in Wayfinder's Guide to Eberron, indicating that the designers intended for you to be able to create multiple copies of the same magic item with the feature. The presence of the word "differet" here very clearly indicates that you could not make two of the same magic item, so this deletion, which very clearly indicates that you can create two of the same magic item, can be nothing less than intentional.