If the videos mentioned in the notice are hosted on Youtube without authorization, then the takedown notice should be sent to YouTube.
If the videos were uploaded to Youtube with authorization, then accessing them through youtube-dl is not an example of the program being used for infringement.
Either way, the purpose of the software is to download anything publically available from YouTube. Its purpose is not copyright infringement unless the purpose of YouTube is copyright infringement.
The monetisation of the content depends on a lot of different factors, many have monetized unauthorized content over the years, many received money from the same unauthorized content by faking clicks and views and many avoid paying YouTube in the form of ads by using ad blockers
I believe youtube-dl users amount to a maximum of a single digit percent of the above (with the digit being between 1 and 2 with 2 excluded)
If the videos were uploaded to Youtube with authorization, then accessing them through youtube-dl is not an example of the program being used for infringement.
Either way, the purpose of the software is to download anything publically available from YouTube. Its purpose is not copyright infringement unless the purpose of YouTube is copyright infringement.