Some times I have found that the Site Actions menu missing when I login even though I’m the site collection administrator. There can be many reasons for this. I found two of them in which the second one was the reason in my case.
- If the the issue occures after a backup/restore of the site collection, the destination server may contain a local administrator users with same name as site collection administrator.
- The site collection minght have became read only. Check it throuh Central Administration website. (Central Administration > Application Management > Site collection quotas and locks)