If they have (strong enough beams), we know that the beams that are there are strong enough for their purpose. We do not know anything about the number of beams!
If they have (enough) (strong beams), we know the beams are strong, and we know that there are enough of them.
Your new third option is interesting. Because beams now separates strong from enough, the sentence means the same as the second one. These two sentences mean the same:
They have (enough) (strong beams).
They have (strong beams) (enough).
However, the second version doesn't sound as good to me. Enough is usually found at the end of a phrase when used as an adverb, as in
I have eaten enough.
Edit: Adding an example I have just used (in a comment on your other question :) )
Let's say we have a bunch of apples, and we want to eat apples. There are two things we want to know about the apples:
- Are the apples ready to be eaten?
- Are there sufficient apples for us to eat?
The first question I can answer with:
- Yes, the apples are ripe enough to eat.
That is good news - now, do we have plenty of apples?
- Yes, there are enough apples.
Now we know we have apples, we know those apples are ripe enough to eat. I can say:
There are enough apples.
There are enough (ripe apples).
There are enough (red apples).
There are enough (nice juicy red ripe apples).
In all those cases, enough just says that the number of objects is sufficient. The objects are all the time apples, whether they are red, ripe or juicy.