Should you give examples of the destructive ways you like to avoid, but as far micropropagation profit evaluation it is basically an application of operation research of linear economic theory as in Paul Walker's https://books.google.it/books?id=NEbrCAAAQBAJ&pg=PA82&lpg=PA82&dq=operation+research+plant+tissue+culture&source=bl&ots=Ve8WVzKEW0&sig=5g5fnb_ZDw_pV2fLv1iKdmdbfL0&hl=it&sa=X&ved=0ahUKEwil1qeA_YrLAhVHuhoKHc4zAeMQ6AEIMTAC#v=onepage&q=operation%20research%20plant%20tissue%20culture&f=false
The success of a micropropagation protocol is generally measured in terms of culture establishment, frequency of shoot multiplication, frequency of root induction in plantlets, plantlet survival during hardening as well as in the field. These does not require and destructive method to measure.
Optimal protocol in woody plants means the best performance at the tissue culture stage (establishment, multiplication, rooting). As we know, most of the growth parameters in these three phases do not need to destroy explants and plantlet, such as the number and length of roots and stems, the time of the first emergence of adventious roots, survival rate, responding explant percentage and etc.