There have also been questions about the ability of Nigeria's justice system to handle so many cases at once and even of simple procedural details such as whether defendants will be tried on their own or together.
The justice ministry itself has already highlighted the potential pitfalls facing judges, such as poor investigation techniques, lack of forensic evidence and "over-reliance on confession-based evidence".
To what extent those on trial are connected to the group will likely come under scrutiny.
"There are good reasons to believe that large numbers of the detainees have very little or no connection at all to the group," Matthew Page said.
Amnesty International said in a damning June 2015 report that more than 20,000 people had been arbitrarily arrested as part of the fight against Boko Haram.
It highlighted appalling conditions at military detention facilities and claimed at least 1,200 people had been summarily killed and 7,000 died in custody since 2011.
The group's spokesman in Nigeria, Isa Sanusi, said: "Nobody knows exactly how many people are detained, if they are still alive and where they are."
President Muhammadu Buhari, who was elected in 2015, has promised to look into repeated accusations of human rights violations, including against high-ranking officers.
At least two commissions of inquiry have been established but the army announced in June this year that no action would be taken against top brass accused by Amnesty.
Such revelations have made Western countries cautious about responding to repeated Nigerian requests for more military support in the conflict, particularly in terms of weapons and other hardware.
The US administration of former president Barack Obama blocked a nearly $600 million deal with Nigeria for 12 fighter planes after a botched air strike that killed more than 100 civilians.
The deal finally went through in August.
Britain's foreign minister Boris Johnson said on a recent visit that London was considering a Nigerian request for more military hardware.
Amnesty's Sanusi believes the mass trials of Boko Haram suspects were the result of international pressure on the Nigerian government as it "desperately wants to procure arms".