I have not seen this problem with nicesplice-cropped recordings, though I have seen it occasionally when playing across a network; when this has happened the playback time on the front panel was wrong. I assumed that it was due to a problem writing to the remote hmt file.
The difficulty with nicesplice-cropped recordings is that there is a jump in the DTS and PTS timestamps at each join. This is what causes the audio dropouts. You can fix this with ffmpeg but it would add to the processing overhead and would not be easy to automate, depending on the streams present, and you would have to patch the original hmt file and create a new nts file.
If you take the nicesplice-cropped ts file and create new sidecars (with sidecar) the recording duration will be incorrect and you get jumps in the timebar when you reach a joined section. If you use the original hmt file, the duration will be correct, but you will run out of timebar towards the end of the recording. It will still fast forward and rewind past the end of the timebar but if you stop playback it will go back to the start when you resume playback.
Is it possible to create a utility to set the timestamps of the next section to be joined to start from the end of the previous section, without remuxing the streams? If so you could then just join all the sections with the 'cat' command. This would fix the audio dropouts and solve playback issues on other devices.