Hi Hive account@kilbride, that's a very good question. I did not find any study on the question, but my guess is that these elements are generally integrated in non-coding regions of the genome or in gene introns, which reduces the risks of potential gene disruption during the transfer. I think that any homing endonuclease that would target an essential gene would have been eliminated during evolution.
The transmission efficiency is definitely not 100%, since homologous recombination is active only during certain phases of the cell cycle and not in every cell type, I think there is a significant proportion of cutting events that simply lead to the mutation of the recognition site of the enzyme, preventing recutting and the "copying" of the gene. The last figure is a bit misleading because too simplified, thank you for raising this question :)