Aliens (or similar "outside" invaders).

Family atomics had been stockpiled for generations in preparation for the theoretical invasion of the Imperium by an outside alien force. From Children of Dune:

[The Great Houses] were undoubtedbly sincere in subscribing to the argument that nuclear weapons were a reserve held for one purpose: defense of humankind should a threatening 'other intelligence' ever be encountered.

It's also worth mentioning that the Great Convention - itself designed in part to reduce collateral (civilian) damage, thereby maintaining the faufreluches caste structure - banned the use of atomics against human targets; their use against structures, such as the Shield Wall or for other theoretical "atomic landscaping" was presumably hazier. But as with a lot of technical concepts in Dune, a lot of this is (intentionally) left vague by the authour.

As for lasgun-shield interactions, it seemed to be implied that using them against human targets went against the spirit, if not the letter, of the Great Convention, though "accidents" occasionally occurred, such as in Dune, when

Not only was deliberately triggering such interactions frowned upon for political reasons; its usefulness was limited by the fact that the magnitude of the reaction was highly variable, unpredictable, and - it seems - random. From Dune:

Jessica focused her mind on lasguns [...] A lasgun/shield explosion was a dangerous variable, could be more powerful than atomics, could kill only the gunner and his shielded target.

This seems to suggest that hitting a shielded target with a lasgun could do very little to to overall outcome of a battle - or it could wipe out the entire battlefield, and then some.

On that note, it's worth mentioning that one of the main purposes of the Great Convention, the forms of kanly, and the fafreluches caste system in the Imperium was to deliberately keep wars small-scale, minimizing casualties, and ultimately keeping the wheels of commerce working consistently [stagnantly, one might argue] as they have for millennia.

As some additional speculation, I always had the impression that family atomics was a bit of Cold War commentary on Herbert's part - the Houses spent resources needlessly on stockpiling these weapons as a show of power, even though they were unusable due to the threat of atomic retaliation. From Dune Messiah (emphasis mine):

The advent of the Field Process shield and the lasgun with their explosive interaction, deadly to attacker and attacked, placed the current determinatives on weapons technology. We need not go into the special role of atomics. The fact that any Family in my Empire could so deploy its atomics as to destroy the planetary bases of fifty or more other Families causes some nervousness, true. But all of us possess precautionary plans for devastating retaliation. Guild and Landsraad contain the keys which hold this force in check. No, my concern goes to the development of humans as special weapons. Here is a virtually unlimited field which a few powers are developing.

-Muad'dib: Lecture to the War College, from The Stilgar Chronicle

It would take some time digging around for the actual quote. But I believe it was mentioned in the first novel that the ultimate reason of why they were kept was as a last resort, if they ended up encountering hostile alien life that other weapons could not defeat. Then there is the deterrent factor, if one house has them then the rest of the houses (or at least many of them) need to have them in order to enforce the Great Convention's consequences for using them.