Currently, we have 2 different SharePoint 2010 webapps for
Mysite(Personal User Data )
Collaboration Room / Sharepoint Workspace
We are planning to migrate to SharePoint 2016 . We are considering to make a single webapp and below that we will make 2 site collections each for Mysite(Personal User Data ) and Collaboration Room / Sharepoint Workspace .
Can anyone tell me is there any performance issue if we do so ?
There is no performance issue, in fact there is an argument that this actually has less impact as you are only using one app pool instead of two.
I do this regularly with host named site collections and have had no issue.
Saying all that before you do this make sure that there are no solutions or other scenarios that will have a detrimental impact on the other. Also be aware of any SLAs you may have. Is it more important for you to guarantee a higher level of up time for your collab sites etc.
Keep an eye on your performance and make sure to baseline but this really applies to SharePoint in general...
What do you intend to do is called HNSC (Host name Site collection) that mean avoid creating multiple web application with multiple application pool,
This is very useful for performance , So there's no issue for performance with this method. for more details check The Expense of Application Pools
But I think the main issue will be related to capacity planning , where the two site collection will be created in the same content database, so you should limit the number of site collection at the content database
Then create a new one that you hold the second site collection. To lock down a content database check Content Database Consideration
In my humble opinion , In your situation , you have My Site host , so I suggest creating two web applications with the same application pool
My site.In this case, you cared about performance, capacity consideration .