Australia managed only a solitary gold to Emily Seebohm, who successfully defended her 200 metres backstroke title, and finished eighth overall on the medals table headed by the dominant United States.
The meagre haul came less than a year after Australia's Olympic team arrived in Rio with eight of the world's leading times but emerged with only three golds after a number of their top hopes crashed out.
The Budapest blow-out will do little to allay concerns that Australia's top swimmers wither in the spotlight of the major events but Verhaeren said he was "very proud" of his team's efforts in Hungary.
"(This result) reflects where we are at and where some of our medal contenders are in terms of their preparation," the Dutchman said in comments published by The Australian newspaper.
"I'm absolutely very pleased with the rookies and the performances they set and the steps they made into finals, into records, into personal best times.
"I wouldn't want to use the words happy or satisfied because that would mean we were at the end of the journey when it's the beginning."
Australia's Olympic 100m freestyle champion Kyle Chalmers missed the meeting due to heart surgery, while former 100m world champion James Magnussen skipped it to preserve himself for next year's home Commonwealth Games at the Gold Coast.
Former 100m freestyle world record holder Cate Campbell also elected to sit it out, while her sister Bronte's title defence in the sprint was hampered by shoulder injuries.
But there were some notable setbacks, with Cameron McEvoy missing out on a podium spot in the 100m freestyle and Mitch Larkin crashing badly in his defence of both his 100 and 200 backstroke titles.
Australia's failure to medal in any of the men's relays was also a surprise and sparked criticism of the team's tactics by absent swimmer Magnussen.
Verhaeren, the former coach of Dutch greats Peter van den Hoogenband and Inge de Bruijn, has pushed Australia's swimmers to compete in more events outside home pools after Rio, where the team's failure to meet expectations sparked a major review.
He said the different preparations may not have helped all his swimmers at Budapest.
"I think we need to take responsibility for the choices we make and the choices we made this year included extended travel," he said.
"Emily Seebohm and Emma McKeon really like this way of preparing and they swam themselves into the meet so for some that works great. For others it’s more of a gamble."
(Reporting by Ian Ransom; Editing by ....)
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