The wikipedia page about "Glitter bombing" seem to have two meanings, I assume you are going for the "fill the ballot envelope with confetti" one.
In general, messing with the ballot means that those votes would be counted as null votes. As such, it is unlikely that the Australian electoral organization will provide a detail of the reasons of those votes being null, so there will be no direct report of the effect.
Of course, usually accidental1 null votes are a small, fairly constant fraction of the votes cast. A significant increase of that fraction would be easy to spot and, since it seems that there is only one side promoting a boycott, it would be reasonably to think that most of the difference is due the campaign.
Then again, it would not count in the official results and such tactics convey a clear message that the proponents of those measures believe that they are going to lose the voting.
Is that effective? Depends of what the message is. If the message is "We are against this measure" then voting "No" is a more direct, measurably, effective solution. This kind of measure -as calls for boycott/abstention- are usually used to signal a "We do not accept the existence of this referendum/I will not feel bound by anything coming out of it" message that is not available in the ballot.
Additionally there is a legal angle specific to glitter bombing: most jurisdictions do not take it kindly when people or organizations attempt to disrupt the electoral process, and someone caught trying to introduce strange objects2 in a ballot box could3 find themselves in a bad legal situation.
Someone marks more candidates than possible, etc.
2Since ballot envelopes and the ballots themselves are usually rather thin are thin too, it would not be too hard to notice some people introducing ballots stuffed with too much contents.
3IANAL and IANAA(ustralian)L, but I think it is a reasonable possibility. Another question is if people encouraging other people to break the law could be prosecuted, but that would be off-topic and way more specific.