Does ACM have a style guide for authors? I am writing a paper for an ACM transactions publication precisely using the acmsmall format. However, I am yet to find a comprehensive Do's and Don'ts for writers with regards to style. For example, I've seen some papers say, "in Equation (5) ..." while others abbreviate it to "in Eqn. (5) ...". I have also seen some papers merely refer to equations by their numbers i.e. "in (5) ..." as is done in the IEEE. I've even seen these used interchangeably. 

The first case is correct though, as it was used in a sample paper provided, however, are Eqn. (5) and (5) acceptable equivalents?

There seems to be consistency in referring to figures and tables though: figures are always referenced thus "in Figure 5 ..." and never abbreviated, for example as "Fig.".

At the moment, I'm just picking styles from already published papers which I'm not sure is the best way.

So where does one find clarification on these issues? Which is right in the above cases mentioned?
You should take a look at the format that the ACM template gives to you, but there is no straight answer for an specific format. Try to focus more on the content (like they have advise you on one comment) that in the format. Actually I have seen in some ACM published papers that they put things like (considering your example):


In Equation 5... or
In Eq. 5 ... or
(put the variant you think here)


Consider that is one of your least worries, if you had some problem with the format the reviewers will point to that, but if the content is good is what really counts.

Good luck!