There are a few ways of dealing with enemy AMMs of differing levels of cheese.
1: Use size 1 missiles to bleed the enemy of AMMs. There are a couple variants of this, box launcher size 1s as your main attack, you are committing to having fairly short range on your missiles, period. Or use outright decoy missiles. If magazine space is a premium, have a missile that is either nothing but engine, or perhaps .51 MSP armor and the rest engine (and fuel). If missile cost is more a problem, create a bunch of missiles that have .3 power engines, the cheapest possible missile you can make. Either fire them from a waypoint, or if you have oversized fire controls and sensors and/or a forward observer, use that. If you fire decoy missiles in single missile volleys, spread out over time, you can often make the enemy waste 3 AMMs killing a decoy that cost 1/10 or less of what a regular 1 MSP missile cost.
2: Discover the range of the enemy missiles and dance at the edge of it. Draw fire, they retreat out of range so that they explode pointlessly. Alternatively, probe their AMM range with a shielded warship and simply have it retreat once it has taken some hits. This works if you have less precise information about the exact range of their missiles.
3: For beating static defenses, there is time on target missiles. Assuming you know, roughly, the range that AMMs will be used against ships, you pick a 2nd stage that separates somewhat beyond that range, with a slow first stage. You then fire hundreds upon hundreds of missiles from a ship moving at the same speed as the first stage, so that they all separate at the same time. Then, instead of trying to defeat the enemy magazines you are attempting to overwhelm their fire controls.
4: Use wild weasels to beat the enemy missiles with sheer speed. A downside is that the enemy won't fire more missiles than it thinks will kill the target until the missiles run out of fuel, so you would have to do a lot of fuel intense and micro intense maneuvers to run them out of missiles.
5: Have cloaked point defense ships whose cross-section is significantly less than 50 tons. Have them group with the occasional sacrificial ship/fighter with cross-section greater than that. So if the enemy actives can detect a 50 ton ship at 20 million km, but your cloaked ships have a 30 ton cross-section, they will have a significant margin. If your point defense is sufficient to protect whatever is targeted, they can bleed the enemy of missiles that way, while staying out of range themselves. You can also bleed them of anti-ship missiles by pairing railgun fighters with larger ships, bleeding them of anything linked to an anti-ship fire control.
6: Least cheesiest, simply have enough point defense to reliably shoot down their AMM volleys. It is more expensive, and there will likely be some leaks. Then, you won't need long ranged missiles at all, but can have missiles that have more boom per BP.
