Mods that just include with a modified PROGS.DAT file. This means that the modification cannot be modified in any way, nor can additional modifications be added. Reasons this may have been done vary. For example, it could be that the author was unhappy with the modification in its current form and wished to further work on the mod before releasing it to the public.
Furthermore, this method also guarantees better stability than an open-source modification in the event the latter lacks a PROGS.DAT (due to download size limitations in 1996). While one can be generated for an open-source modification in the event it doesn't exist, there is more room for user error in comparison to the plug and play nature of the closed-source modification.
Note that there are cases where the modification is closed-source, but upon request would be provided the source code. This is still considered closed-source due to the general inaccessibility of said code.
Note that there is no such thing as true closed-source modifications in Quake. Every modification can be decompiled with the proper tools, it just is a far less user friendly experience than the average mod. These decompilers can come with caveats of their own however, such as outputting to another language which makes it harder to determine what changes have been made to each individual file. This means that it requires more experience to alter these files and is not officially supported in any way by the mod author.
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