It remains difficult to imagine the seminal nature of atoms and void over eternity. For that matter, it is difficult to imagine eternity!
I think that difficulty to which you refer has got to be part of the reason that Epicurus ended the letter to Pythocles with this:
All these things, Pythocles, you must bear in mind; for thus you will escape in most things from superstition and will be enabled to understand what is akin to them. And most of all give yourself up to the study of the beginnings and of infinity and of the things akin to them, and also of the criteria of truth and of the feelings, and of the purpose for which we reason out these things. For these points when they are thoroughly studied will most easily enable you to understand the causes of the details. But those who have not thoroughly taken these things to heart could not rightly study them in themselves, nor have they made their own the reason for observing them.
And I presume part of the thought process there is that the only way to get comfortable with thinking about the issues involved with infinity is to think about them on a regular basis, and so by doing acclimate ourselves to the issues, just like with mortality / death.
If we wait til we approach death to think about death, or if we wait til some priest or academic philosopher hits us with some tricky question about infinity, then we're much less able to deal with those problems than we would be if we had engaged in regular practice.