I would not be surprised if one did a timeline analysis of the project you would find something like the following. At the time of the ship design and competition, the Eurotorp was much better than the Mk 42. Mk 54 wasn't really prime time yet when the decision was likely made. Given the time lag on the project it was probably cheaper to just keep going with the Eurotorp then change anything. Its a very good torp.
The fact Australia has stuck with the Eurotorp likely means it has better performance in X number of categories (shallow water perhaps) or the juice isn't worth the squeeze to switch. Maybe during the Hobarts midlife they will look at a system that is torpedo agnostic and will shoot whatever you put in it. Canada bought such a system for the Rivers.
Having looked at the timeline, things a look a bit different. JP2070 (the Australian LWT replacement programme for the ADF) had the Phase 1 RFP close in July 1999, per
this ANAO report from 2010.
AFAIK the Mk 54 LWT the US developed as a replacement for the Mk 50 and Mk 46 (which was originally to be replaced itself by the Mk 50) started developmental testing in July 1999, so I do not believe it would have been possible for a Mk 54 RFP to be submitted. The Mk 54 itself was developed in part due to the high costs of the Mk 50, as well as to improve upon weaknesses in the Mk 46 which was really designed for blue water usage and not in littoral areas.
The MU90 does appear to have a greater max depth, as well as higher max speed. Other areas of performance are not known publicly. One thing which is definitely different though and could explain why vessels designed to use MU90 were not changed over to Mk 54 has to due with the LWT propulsion and power source. The Mk 54, like the Mk 46, uses the liquid Otto II fuel whilst the MU90 uses a battery. As a result of the Otto II liquid fuel, the magazine where the LWT's are stored need to be designed with that in mind. When the
Hobart-class DDG's were being built, the expectation had been that embarked naval helicopters would use air-launched MU90, but with the select of MH-60R Seahawks as well as P-8 Poseidons, Australia found itself with the Mk 54 LWT to launch from aircraft. This triggered a need for the hangar magazine in the DDG's to get redesigned since they were not original designed or built to accommodate Otto II fuel.
The impression this left me is that one of the major issues with LWT selection is not which system to use to launched the torps, but in different torpedoes having different fuel/power properties, which leads to different requirements in order to safely handle and store the torps aboard ship.
If Australia already has a stockpile of MU90's, and it would require a redesign and refit of RAN destroyers to have them entirely fitted out for the Mk 54, I could easily see the MU90 being kept in service until they began expiring.