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I don't think this can easily be answered without additional information. I would consult IBM documentation that discusses proper sizing based on the amount of users, their workload profile, and any additional databases you have on the server.
More than likely there is "no one size fits all" type answer.
1. How many vCPUs should be allocated for a VM running a Lotus Domino server?
2. What are the maximum number of vCPUs it could possibly use?
3. Based on how it is configured out of the box, what would be the default number of threads it would be using - 1, 2, 4?
question 1: there is not enough information to answer this question, the sizing of a Lotus Domino server depends on many variables. like how many mailboxes, average mail throughput, how many databases. etc. therefore check IBM documentation of generic sizing guides
Question 2: this again depends on yout vSphere license type for all versions other than Enterprise plus it is 4 vCPU for Enterprise plus it is 8 vCPU.
Question 3: again a question that cannont be answered as it depends on the phyiscal CPU in the Host server