Of course it’s slower. Your using https to do something that’s meant to be raw binary. The overhead is killing you. Something like iscsci, is pretty quick compared to https as a storage protocol.
If random access is needed in a cloud environment, use either that local ephemeral SSD, or a cloud block device which is probably just an iSCSI implementation underneath, or at least a close equivalent.
Operating fleets of compute and IO in cloud environments means that POSIX semantics generally work really well for genomics.
Folks that have reimplemented basic genomics algorithms on top of protocol buffers standardized serialization still store them as BLOBs, and have not delivered benefits that can be realized in publicly available compute environments.
Put another way I've seen extremely low-latency https servers. The latency in S3 doesn't come from using https.
I highly doubt HTTP has less latency than that.