In an alternate universe we have nice specialised GUI front ends on things like netCDF or SQLite that enable what you say. Or hell, just a spreadsheet-like view over a real database (but with actual names as columns). All the GUIs I have seen are really not up to the task for typical scientific data. They are clunky, heavy, slow, and difficult to use for visualisation. We are not writing new front ends for every type of data, and nobody seems to have written a decent one that could be universal.

Myself (not genomics, but Excel is also some kind of universal medium here as well), I store my data in SQLite files (extracts and summaries anyway; complete datasets take several terabytes), which makes retrieving complex information a breeze. But it needs to be documented and you need to be comfortable with the command line and do any kind of visualisation as a supplementary step. I know of a couple of colleagues doing the same, but we don’t use quite the same format, so data exchange is problematic. I use this setup mostly because I need it to work on remote HPC clusters in addition to a bunch of local workstations, and Excel is out of question there.