meet.jit.si offers a service free of charge through browsers and its app. Its terms of service suggest you can use the service offered free of charge but must not hack or modify the software and service. Please refer to meet.jit.si Terms of Service.
Integrating jitsi technology would be a different matter: You can use the projects free of charge and self-host. If you want to know how to integrate or take advice on bespoke solutions, these can be requested on 8x8.vc, the commercial operation that develops, funds and consults on intregations and bespoke solutions, e.g. app development.
Self-hosting would give you total freedom to use the project software of jitsi, jicofo, jigasi and jitsi-videobridge as well a jibri but you would have to pay for hardware, maintenance and traffic.
So the decision would depend on the app design and usage of conferencing and recording features. The numbers you have indicated still allow for wide variations and more specifics would be needed to assess and estimate cost and limitations. So you need to give some indication of what exactly the 3500 students would do when and how as well as what the app and any potential chairs or seminar leaders would be doing. Many questions would need to be explored so you get specific quotes and solutions.