I share the concern expressed about growing incompetence in the biblical languages. However, I respectfully disagree that biblical language software tools should shoulder the blame.
First, primary responsibility lies with the users--fallen human beings who misuse & abuse helpful tools to their own detriment. Second, languages are really tools for communication & for learning from others & regardless of culture or time period only a relatively small percentage of adults would be sufficiently interested & motivated to go out of their way to spend years to master these tools when the majority are usually more interested in the ideas &/or their practical application--most will always gravitate towards shortcuts to get at the ideas & their application more quickly, e.g., through translation & other tools (including biblical language software tools).
Third, larger environmental forces & pressures have long been at work to marginalize the importance of the biblical languages in seminary training (also in religious departments in universities--I am only commenting on an American context here in what follows): (1) the decline of American public education, such that many Americans graduate high school with deficient reading skills & knowledge of English grammar (also most Americans basically come out of high school monolingual even if some kind of foreign language classes were required as these courses were often taught in a deficient way); (2) humanities & languages generally get the short end of the stick in the face of budgetary cuts & prioritization at all levels of education in modern American society; (3) religious institutions in particular have long been reducing or eliminating biblical language requirements in various programs for various reasons, including an increasing bent towards practical ministry & economic pressures.
There is little that can be done about these larger environmental forces & pressures, except those of us with children can ensure that our own children will be better equipped (through home schooling or private schooling that includes high quality training in classical languages & various modern languages). For PhDs in biblical studies, I think concerted & well-thought comprehensive plans need to be put in place to uphold competence in biblical languages, including increased & perhaps separate courses & training (as compared to what is required for others not pursuing this track) as prerequisites for entrance into a Ph.D. program & additional training after admittance.
Biblical language software tools can also be part of the solution, rather than a problem, even in the training of PhDs in biblical studies. Instructors & professors need to adjust & adapt their methods to take advantage of increased possibilities for training afforded by these tools. The key is to go beyond traditional isolated drills on parsing, grammar, or word for word translation & to use these tools to push students to read larger chunks of texts & to drill them on integrating parsing, grammar, interpretation, & intelligent translation. In addition, for lay people & even people in ministry who never master the biblical languages, biblical language software tools can open up the biblical text to them in a way previously impossible--the solution for giving them better & less one-sided information is to improve & expand on existing software tools, to include not just "what" but "how" & "why" information--not just one person or one group's conclusions, but step by step replicable methods & reasons/arguments, including the presentation of alternative views. So, in my opinion, thus far not enough time & resources have been invested into producing high quality & multi-faceted biblical language software tools that can bridge the gap between interpretation & theologizing/application.