I have started to protect certain site admin areas using a HTACCESS password (installed via Akeeba admin tools) which has led to a critical problem with J-Cook components.

As the helpers are stored in the ADMIN folder which is protected by a HTACCESS password, this means that front end views get prompted for that HTACCESS password if they need a helper.. i.e almost all the time

Can we have helpers for front and backend mirrored in both areas or moved to the site section rather than admin section

Interresting point.
How the other component does ?

Putting the helpers in the front is an heresy. This would break the joomla conventions, no ?
And this might be the same problem for many other files. MVC supperclasses...
Even inheritance would not work. This is a big deal.
Copy and paste the code is very bad idea. I cannot do that.

What happen with your models in front, they are based on superclass localized in the administrator folder as well.
There might be another solution I guess.

In case if inheritance work, just create a front helper that inherit from the back-end file. (same than MVC)

I am very interrested to know more about that.