Direct update would be okay only if instructed to do so by Oracle support. Usually, we use APIs to update EBS tables.
Please see "Manipulating Oracle E-Business Suite Data" from http://docs.oracle.com/cd/E18727_01/doc.121/e12897/T302934T458264.htm
We strongly recommend that you do not manipulate Oracle E-Business Suite data in any way other than using Oracle E-Business Suite. Oracle E-Business Suite tables are interrelated. When you use Oracle E-Business Suite, any changes made to the data in the Oracle E-Business Suite tables are validated, and any relationships are maintained. When you modify Oracle E-Business Suite data using SQL*Plus or customized applications components, you are at risk of violating the audit ability and potentially destroying the integrity of your data. You must be aware of the potential damaging problems that improper customization may cause.