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With links, this limit is not existing; but of cause there is a danger in the fact that links can end up being more of a mesh that a strucutestructure.

Some other Apps like Issue Links Viewer or Pathfinder can help visualising the linking.

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Im sure that removing or disabling subtasks can cause fustration for hardcore and experienced users of Jira, so do always remember to argument and educate for the solutions You implement. Its all a matter of the way people work and are educated to use Jira ....

All good?

Of cause not. Not using subtasks has some drawbacks, one of them being worklog and the presentation on the parent, where all work on this and subtasks can be seen and measured..

Real life story

Some years ago - Ive created a sub-task issue type called Sub-change