The original form of Batch File processing was indeed deprecated from V11.5 (iirc)
I suspect the were a number of reasons for the decision some of them forward looking in terms of under the hood changes and other matters.
I would be surprised if some commercial considerations went unconsidered.
There are some options for different levels of back end automation of Monarch processes whether Classic Monarch or Data Prep Studio as it advances in functionality.
As for the licensing costs I cannot comment as I don't know. I would suggest you or your software purchasing people contact Datawatch to discuss it.
Bear in mind that in certain requirement situations entire organisations have been almost entirely run on the basis of reports produced and automated (in the old way which was quite technically intensive) by one person. A newer approach where fewer technical skills are re required and the system can be created and supported without so much effort may just be less expensive and more deployable as well as, potentially, more secure and less exposed to a single point of failure (the loss of the person who developed it).
Just something to consider generally, although it may not have particular relevance in your situation.