We expect to have ElasticSearch for Magento Search on Hypernode soon. Keep an eye out for the announcement on our changelog (https://support.hypernode.com/category/changelog/).
This way it would become unmanageable by Byte, you would have "Hypernodes gone wild."
There is now way to keep track of customizations on Hypernodes.
If there would be a problem, they simply cannot upgrade your platform anymore.
If you have a specific questions about a service you would like, you could create an idea for that and we could vote for that
I think that there is a problem with the specific module, whereby it does not reference to the linked file in the /skin/adminhtml directory but to the realpath in .modman
Files should be linked correctly from within the module modman files to their proper directories.
This way this problem would never exists if you use the right Magento functions.
I should never recommend to publish dot-directories.
I hope that you mean SFTP by this, I would recommend to never make use FTP on my Hypernodes.
Maybe there is a possibility to have some jailed accounts which can be put in limited directories.
I have my Magento installations installed in htdocs and thereby placing composer files outside the document root.
Ofcoarse this means I've linked /public to this location, but security wise I would never run in problems like these