Are there disadvantages to this method of testing building wiring after a lightning strike?
An arc fault circuit interrupter will reduce the probability that an arc fault event will result in a fire.  It does not guarantee that arc fault events will not cause a fire, nor will it protect against all other kinds of equipment damage.

Further, one advantage of doing the high-voltage test is that it ensures that if damage occurs while the property is owned by someone who has insurance, responsibility for repairs can get properly assigned to that insurance company.  If the lightning strike had damaged the insulation to the point that it would arc destructively the next time it reached 1.5x normal voltage, such a condition might not get noticed for years even with arc-fault interrupters installed.  If the property had been sold before that occurred, it may be essentially impossible to hold responsible the company that insured the property at at the time of the original lightning strike.

Note that insurance companies view risk somewhat differently from individuals.  From their perspective, it's better to spend enough money to definitively resolve a claim than to spend a lesser amount to "probably" resolve it.  While I've never had to file such claims, I would expect that many insurance companies would rather pay the cost of such testing and know immediately whether they would or would not also have to absorb the costs of repairs, than install AFCI devices and hope for the best but never really "know".