I think it entirely depends on the goal/purpose for the resulting digital files. Are they to be actual, near-identical representations of the physical tapes? If so, it might be best to make each side a separate digital file (as you’re doing) — because each side was originally “separate” (plus, content might also be more easily discoverable by future users). Or, is it more content-driven? For example, do the two sides present a single show/program? If so, it would seem to make more sense to combine them into a single file (so future users could easily find the specific program or show they’re seeking).
In this sense, I would think consideration also should be given to the anticipated future use. You mentioned some of the digital files are ultimately destined for Missouri archives. Whether this refers to an academic institution, state broadcasters association, or something else, I cannot tell. Either way, however, it sounds like they’re for archival, “historic” storage purposes (for use, potentially, by future documentarians or historians, possibly). If that’s the case, then separate files for each side would seem most appropriate.
Conversely, if presenting complete programs/shows today is the goal, a single file of individual programs/shows (combining the cassette sides) would seem highly appropriate (plus, in this scenario, I’d also see no reason to not remove the “gaps” from the leader tape). That’s what I’m doing here, in presenting today old airchecks — of distinct individual shows — from my former all-request radio show:
The Jukebox: Radio Archive (June 19, 1999)
For this podcast — which presents full shows — I even add “swoosh” SFX whenever audio is cut off (due to cassette tape running out), as in this example. Plus, in show notes for this episode, I even included the following explanatory note:
05:42 Tom/Rochester (“All I Have To Do Is Dream”) (Note: Cassette tape ran out in the middle of this phone call; it would seem as though I flipped over the tape during on-air playback of the call)
In summary, I’d say it mostly depends on how you foresee future users using the files.
