How common is the character 唷 (pinyin: yō) in Mandarin?
Major dictionaries published in mainland China usually have the official Pinyin chart as appendix.

You can download the official pdf of the Pinyin system from the government site: http://www.moe.gov.cn/ewebeditor/uploadfile/2015/03/02/20150302165814246.pdf 

You can also find it on wikisource: https://zh.wikisource.org/zh-hans/%E6%B1%89%E8%AF%AD%E6%8B%BC%E9%9F%B3%E6%96%B9%E6%A1%88

You also need to have a basic understanding of Chinese phonology and the Pinyin system. For instance, when there is no initial, finals beginning with 'i' should be written as 'y', and finals beginning with 'ü' should be written as 'yu'. Hope this clears your questions about yo is in the slot for "y+o" but in this article, it mentioned as a combination of i+o and some charts don't have "yun" but there are clearly hanzi that use it. 

In my personal experience, the character 唷 is not very commonly used. 哟 is perhaps more common. 

On the whole, interjections are often exceptions from phonological rules. (Think of the English word 'hmm'.) In Chinese, the pronunciation of interjections are often fluid. If a sound combination is only used in interjections and no other character uses this sound combination, it could be considered not part of the normal phonology and thus is not included in the Pinyin chart.