There's two I've seen.
1. Just reduce the number of different types of bonuses. That way its still possible to hunt for a few, but it doesn't turn into the 3e stack-a-million-bonuses thing. This is the PF2e approach.
2. Diminishing returns. Shadow of the Demon Lord has what are called boons and banes. A boon adds +1D6 to the roll; a bane subtracts -1D6. You can have multiples of any of them but you only get the best. So if you've got three boons on your attack roll, you roll the D20, roll 3D6, and add the best of the D6 rolls to the value. It means its still somewhat useful hunting for multiples, but less and less so.
Edit: And to be clear, I don't really care how smoothly it works; it produces a result I don't like twice over; it makes only bothering with the first benefit what you do, and then it makes it matter too much.