You make a good point. Leaving one’s faith leaves one potentially feeling empty or lost because a relationship between them and their god(s) has died. Relationships are certainly important for humans; they provide meaning, an additional set of priorities (need to by flowers for Valentine’s day for your partner or pray x times per day to your god(s)), and exist as their own entity. This is why we grieve the loss of a relationship the same way we grieve other losses. But just like the end of any other relationship, it gets better with time and new meaning will replace the old.
This is only a problem with those who perceive that they have a relationship with god(s)/spirit(s)/the universe in the first place. The emotional void you describe is not felt by the majority of long-term atheists because they’ve filled that void with new meaning. Especially as more children are being raised as atheists, who don’t have this void to begin with, this currently valid point will become less valid with time.
Personally, I’m very comfortable with my perceived place in the universe. I have a very tangible relationship with nature through the natural forces acting on and within my body. I was raised christian, but the stories of the bible seem unimaginative and dull compared to the immense beauty of the scientific explanations of nature.
For example, my body is composed of stardust and after death my body will return to nature and take part in countless future natural events. After death I’ll be part of a tree, part of other animals, and maybe part of other people who eat those plants/animals and incorporate the matter that was once my body into their own. Furthermore, I share a common ancestor with every other living thing on the planet—now that’s a relationship!