Yes!

I believe the accepted thinking is we fail to grow most microbes as laboratory isolates and as such most of what we historically know about the microbial world is confined to the small minority of microbes we can actually grow.

The reasons being things like specifics of their niche, them being members of interdependent microbial communities, etc. NGS and the subsequent development of metagenomics has given us a window into this microbial diversity. It is particularly the case in complex interdependent niches (e.g. rumin); we can use NGS to characterize the microbiome of a ruminant (a cow e.g.), and changes to that microbiome based on diet, disease or genetics, but we can't grow most the individuals of the microbiome as isolates in the lab.

One could argue, for example, that many of these microbes are obligate symbionts and we cannot replicate the conditions of their symbiosis in vitro.

I agree with the above answers that there are many organisms in nature we are not able to grow in the lab. I do not think that we understand why and it may be for a variety of different explanations depending upon the organism.