For an automatic observation (without a human intervention) I thing it's better to install Ekos int the remote site, since you eliminate one point of failure (internet connection). 
Also, this allows you to connect from different locations/computers without having to install/configure Ekos in many computers.

On the other hand, the indi webserver option provides more security if multiple users have access to the telescope, avoiding any uauthorized user mess up the remote computer.

Take a look to Indihub (indihub.space) , and may give a try to taste what indi webserver can deliver.

 

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