etymonline doesn't note that nowadays ever had a spelling with hyphen but I found a few random sites claiming that it once was hyphenated. Was it ever spelled as "now-a-days"?
Google Ngram has an answer for you here The hyphen-free form is significantly more common than the hyphenated form. Google Ngram plots the frequency of words and phrases as a function of time. As you can see from the graph, nowadays is significantly more common than now-a-days".
The OED has citations showing the adverb spelt as nou adaies, now a days, now adaies and now a days. There are just two showing the hyphenated now-a-days, and one showing the adjective as now-adaies.
I have certainly seen it spelt now-a-days, but this spelling is not common. This is not so much a matter of etymology as it is one of convention.
But is the phrase itself best spelt with hyphens? Let us examine it.
If we take the basic phrase nowadays and separate it, we get three parts: now, a, and days.
The adverb now requires little explanation, as we have seen that it was merely appended to the earlier word adayes.
Though I cannot say with absolute certainty, based on similar adverbs and prepositions (which have more in common than one may think), we can assume that the a- from adayes is the same as that in aboard, atop, around, and so on. This a- usually represents a reduced form of on (climb aboard the ship is shortened from climb on board of the ship and so on). Convention does not use a hyphen in this construction; with this observation, we can conclude that no hyphen is required between a- and days.
For some further prodding, we can look closely at the final element days. This, when we look at its Middle English form dayes, is evidently from Old English dæges, the genitive of dæg 'day'. Thus the word, in itself, means 'of day'. In Old English, dæges was often used to mean 'by day'; this usage continues to the present, as we will still say 'I work days' to mean 'I work by day'.
However, the last two elements as a whole form adays, which may be an alteration of Old English on dæge 'today'. The word today, which in the past was hyphenated as to-day, was ultimately an alteration of on dæge, a dative construction. Prepositions can often take multiple cases; it would not be surprising that on should transfer from dative on dæge to genitive on dæges. From this we should get adayes, but, as we've seen in similar words, there is no reason to hyphenate it as to-day and to-night once were.
In conclusion, there is no obvious reason to hyphenate the phrase. If anything, the most logical way of spelling it is now adays, but, considering that the second part adays is no longer used, this is inadvisable at best. Yes, it is occasionally hyphenated; no, it was never customary to do so, as we can see from the etymology: on dæges simply compressed into adayes before hyphens came into common use, and no one saw fit to reverse the process.