A better definition of ascribe there than the one you listed, relating to causality, would be one relating to attribution generally.
To ascribe a characteristic to a thing is to state that the characteristic is an attribute of the thing.
For example.
Ice melts at room temperature.
I've ascribed the characteristic "melts at room temperature" to ice.
Ice is translucent.
Ditto, with "translucent".
Now to the gist of the sentence you quoted.
Glass is translucent.
Glass melts at room temperature.
I've (fallaciously) ascribed the attribute "melts at room temperature" to glass by virtue of its similarity to ice in respect to translucency.
P.S. The pattern of the verb can take either of these two shapes, with the meaning being the same in either case:
To ascribe a characteristic to something
To ascribe to something a characteristic.
Your sentence
Whenever men notice some similarity between two things, they are wont
to ascribe to each, even in those respects in which the two differ,
what they have found to be true of the other.
follows the second pattern:
...they [men] are wont to ascribe {to each [thing]} ... {what they have found to be true of the other}
what = that (characteristic) which