I am really not an expert and barely understand this, but I think you need to give them the two W9's. The reason for this is that the Canadian bank uses the information in a slightly different way than a US bank (for which the W9 instructions were written) would.
A US bank uses the TIN from the W9 form to report income from the account to the IRS. The reason they only need one TIN for this is that the bank has no way to apportion the income among the individual account holders' TINs so they just assign it all to one of them. In the very most common case, that the joint account holders are also filing a joint tax return, this makes no difference, while in cases where the account holders are filing separately the account holders file some extra paperwork with the IRS to justify a split of the joint income between them (not that I know what that is, I've not done it).
A Canadian bank, however, does not report income directly to the IRS. It instead reports the income to the CRA along with the SINs of all account holders and, in the case of US persons, the corresponding TINs from the W9's. The CRA, in turn, uses the W9 information to report information from each US person's Canadian tax return to the IRS, including the income from the account.
The difference this causes comes from the fact that, as you'll know, Canada doesn't do joint tax returns. The account holders must instead divide the income from the joint account among themselves for the purposes of filing their separate returns. I believe it is this separated income that the CRA reports to the IRS, so they need all the TINs to separately report the income the way it is attributed on the Canadian returns (this also allows them to separate out the income of a non-US-person joint account holder, which is none of the IRS's business).
So the Canadian bank needs the TINs of all US person account holders so the CRA can report their shares of the account income to the IRS separately. Hence the multiple W9's. This separate reporting makes no difference at all if you file a joint US return since all income ends up in one pot anyway; if you file separately you will likely need to split the account income the same way you did in Canada.
I hope this makes sense.