I finally found the root of the problems on my machine: LimeSuiteNG choose a very low batch size, amounting to
mRx.packetsToBatch == 1
causing packet losses. As a “work around” I manually force the extra config to
strcfg.extraConfig.rx.packetsInBatch = 8;
This results in smooth operation with very low CPU utilisation and no data losses. (Tested with 4Msps over a period of 10 minutes, while doing email and internet surfing and no escalated privileges, i.e. as a normal user.)
I also tried with lower values, (e.g. 5) but then USB bulk errors started to be thrown which made it hard to even abort my test program.
I do understand that a higher value will increase latency, but possibly 100usec is a bit too optimistic. In my case the 8 packets are an equivalent of approx 3ms.