Theoretically, there is no limit on number of applications (and therefore of application instances) in a domain. Practically factors like CPU/memory resources, network bandwidth, application data location, file-based or DB-based domain etc. can affect the Admin server performance. Thus the actual limitation on the number instances comes from the resource availability. TIBCO support suggests the customer test this in their environment and determine a suitable maximum.
For the typical environment we normally recommend a maximum of 150 applications per domain, which means at least 150 deployed instances. Having all the instances combined into a single application does actually make the job easier on Admin. Therefore there shouldn't be any problem, especially if this is the only deployed application in the domain.