Other than checking off each alert from Company/Alerts manager, i see no way to remove them. but if you are talking about Reminders, there is a preference to not be reminded but this does not affect alerts.
You could try this too: http://support.quickbooks.intuit.com/support/Articles/SLN41603
Solution 2: Turn off background […]
Resolution for 'Alerts installed issue: 'Remove default Alerts installed by QuickBooks' available: Yes.
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