Since all systems are within your organization, I would go with 1 queue manager. The big mistake people make is to try and share queues, channels, UserIds, etc. between applications.
The first thing to do is setup channel authentication (CHLAUTH) rules and enable connection authentication (CONNAUTH), so that you have proper MQ security in place. Since all systems are internal, you may or may not want to use TLS/SSL on the channels for data encryption between clients and the queue manager.
Don’t look at everything from 30,000 feet but rather break everything down to individual applications or micro applications. Assign each application their own queue, channel and UserId. Absolutely, positively, do NOT share channels or UserIds between applications.
Create a naming standard for your queues and channels, so that it is easy to identify who they belong to. I like naming things by division/department/group/function/component. Hence, it forms a nice tree of what you have defined and applications are using.
Note: I’m not a big fan of putting queue manager name or hostname or MQ object name (i.e. QUEUE or CHANNEL) in the name of channels or queues.
i.e. Channel names:
HR.PAYROLL
HR.RECRUITMENT
HR.TRAINING
i.e. Queue names:
HR.PAYROLL.TAXES.FEDERAL
HR.PAYROLL.TAXES.STATE
HR.PAYROLL.TAXES.SOCIAL.SECURITY