So, after all - I came up to model quality I strived for.
There were multiple issues I had to fix to get the result.
First, yes, there were overlapping faces on top and bottom parts of model. Model was double-faced there, and this lead to strange lightmap on top of central part. There were interrior faces too. So, I had to remove them all and rebuild remaining faces.
If you use Blender, there are nice options like Remove Doubles and Select by Trait → Non manifold geometry that will help you to fight with surpluses on model.
Second, my UV map wasn’t ideal. To be more exact, there were some faces on UV map, that occupied less than 2 pixels on lightmap resolution. Because of this, lightmap didn’t deliver any useful information for this faces to model.
I had to rebuild UV maps multiple times to get reasonable result. On Blender, I came up to generating UV maps separately for top, center and bottom with Smart UV Project. And then I manually scaled and placed resulting fragments. Don’t forget to set appropriate Island Margin option when you generate fragments. (I set it to 16/2048 meaning 16 pixels on 2048 size, knowing that the actual margin will be approx. twice less when I scale fragments).
Makigirl, thanks a lot for your comments and your time! You set me on the right track with this explanations.
After lightmap issues were solved, I experimented with polygon count for a while. I found ZBrush Decimation Master very useful at generating simplified meshes. It gave me some nice decimation with perfect balance of details and simplicity:
And now model looks like this:
while taking approx 1000 polygons.
Thanks once more.