Suppose that the distance between A and B is 1m, is it correct and natural to say
A and B are spaced by 1 meter
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As pointed out by @J.R it seems that spaced by is a correct expression.
Here is another variant:
According to Oxford Dictionary, you can use the particle apart instead of by.
Position (two or more items) at a distance from one another.
the poles are spaced 3m apart
Using spaced by x where x refers to some quantity is actually fairly common in scientific literature.
The black vertical lines are guides to the eye and they are spaced by 0.7 ps.
Each aperture is a few metres across and they are spaced by a few tens of metres.
On the front surface two semicircular electrodes with a radius of 1 mm are spaced by 100 μm.
Absorption does not accumulate between the spectral holes because they are spaced by only a few times the minimum observed spectral-hole width.
It's bad English in the sense that it is confusing and creates ambiguity. Although I can't give you the exact grammatic rules for prepositions (i.e. by), it 'feels' as though there is a word missing from your sentence, hence the ambiguity.
One would normally say: - A and B are spaced 1 meter apart (singular case), - NN are spaced by 1 meter intervals, (generally a plural context) - or by/at/in equally spaced gaps, etc.