I have two theories.  The mass mutating of transactions occured shortly after MtGox suspended withdrawals and the statement by core developers so my assumption is the "mass mutater(s)" are either
a) the same entities which used it to exploit MtGox's lack withdraw system.  Now that the option to stealthily profit from this is gone, they are just using it to "grief the network"

OR

b) it is someone trying to prove a point  ("oh it isn't a problem, and only affects poorly designed custom clients? Well lets just see about that").

Either way the reality is that mass modification of transaction hashes has never occurred before.  But the genie is out of the bottle now, and given the ease at which someone looking to disrupt the network can carry on this modifications I don't expect they will stop.  Casual users are the ones who are most likely to be affected (caught in the crossfire) simply because they may not understand what is going on.  The issues are more of a nuisance nature, and don't present a security risk (outside of those incorrectly relying on txid for unconfirmed tx as proof of transactions) but they do make the system as a whole look bad (likely the intent of whoever is doing it).