If the company uses S/4HANA, yes, there is the risk that customers will not be able to use LE-TRA after the use rights for the compatibility pack expire.
For SAP ERP my understanding is that the company can still use LE-TRA after 2027. The downside, of course, is that they probably will be paying more for support (extended maintenance is until 2030).
What are the chances that the use rights for LE-TRA will expire and that LE-TRA won't be used anymore in S/4HANA - I cannot say. Before SAP introduced Stock Room Management (which is a 'lite' version of WMS) one would think that companies who need some basic warehouse management functionality can choose only between EWM and external (also non-SAP) systems, even for very small warehouses with simple processes. Then things changed.
Will SAP provide some 'lite' version of LE-TRA as a replacement in the future - no idea, it would be nice to have more choices, because, if memory serves, basic embedded TM does not cover some processes which companies consider as vital (this means paying for advanced features, and it is hard to defend this if the requirements are considered as simple, especially if you work with former SAP ERP customers).
If there were no concerns about the additional cost of indirect access one would say that some companies may turn to alternative vendors for transportation planning, optimization and processing.
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