Will these small segments got merged eventually?

Elastic Stack Elasticsearch
1

set max_merged_segment to 5gb
set shard_index_buffer_size to 5gb
set refresh to -1.
then most of the shard won't need to merge anymore.
and for sometime, manually refresh some shard. so the shard will be:
5gb, 5gb, 1mb, 5gb, 5gb, 2mb...
will these small segments got merged eventually?

2

shard_index_buffer_size applies to indexing, not merging.
merged_segment only applies to 1.X.

But as long as you aren't playing with merging settings, which you shouldn't need to do in 2.X, then yes, things will automatically merge.