Can I change the settings for multiple mailboxes at a time?

Yes, you can!

First, connect to Microsoft Online using PowerShell. Then retrieve a list of mailboxes that you want to change the settings for. For example, you can retrieve all room mailboxes using the following PowerShell command:

$Mailboxes = Get-Mailbox -RecipientTypeDetails RoomMailbox

To retrieve a list of equipment mailboxes, use: 

EquipmentMailbox

instead of

RoomMailbox

You can then change the settings for these mailboxes using the ForEach-Object cmdlet, where <Settings> represents the settings you want to change, e.g. DeleteSubject $true, etc.:

$Mailboxes | ForEach-Object { Set-CalendarProcessing -Identity $_.Name <Settings> }