The 34 current and former players fear being publicly named if they formally join Essendon in a fight against the investigation into the club's 2012 supplement program.
Federal Court Justice John Middleton on Wednesday expressed concern about the players remaining outside the August trial.
But the players' barrister David Grace QC said they would only join if measures were put in place to ensure privacy.
"The reluctance of players to be involved is solely related to this question of anonymity," he told the court.
Mr Grace argued that their reputations would "suffer irreparable harm" if they were named.
Justice Middleton has indicated he'll make a decision one way or another at a further directions hearing on Friday.
Both Essendon and its suspended coach James Hird are arguing a joint ASADA and AFL probe into the club's 2012 supplements program was unlawful.
During Wednesday's directions hearing, ASADA lawyer Dan Star questioned amendments to the statements of claim that detail the arguments to be put by both Essendon and Hird.
He said the changes, which relate to the claims that ASADA and the AFL improperly conducted a joint investigation, amounted to significant "rolling enlargements" to their argument.
"We're giving deep consideration as to whether or not these (changes) ought to be struck out of the pleading," he said.
"We need to know what we're dealing with."
Hird's lawyer Nick Harrington said his client had only lodged one statement of claim, which featured minor differences from a draft given to ASADA.
He said there was no ambiguity to how both Essendon and Hird would attack the joint investigation, in which players under contract with the league were compelled to divulge information to ASADA.
"It was the contractual power the AFL had over players to get this information," Mr Harrington said.
Any application to strike out sections of the argument would be vigorously opposed.
In a statement on Wednesday, Players' Association acting chief executive Ian Prendergast appeared resigned to the likelihood the players would join the proceedings.
"It seems apparent from today's directions hearing that the court believes the players should be involved in the proceeding, as the relief sought by the club and James Hird will ultimately impact them in some way," Prendergast said.
"The players accept that their involvement may be necessary, and are in discussions with their legal team as to the extent and nature of such involvement.
"Despite speculation as to which players have received show cause notices, the 34 players have not been named, and nor should they.
"The players do not believe that the action taken by the club and James Hird - the involvement in which they resisted - should change this."
Essendon chairman Paul Little said the club was happy with the progress it was making in court.
The matter will return to court for a further directions hearing on Friday.
