Use of more ethanol may precipitate unwanted small fragments and nucleotides. The counterion is very important. NaCl, for example, is not very soluble in ethanol. Its use as a counterion will result in more salt, protein and nucleotides in the precipitate. Use of the acetate salt of sodium can reduce contaminants.
Ammonium acetate is very soluble in ethanol.
It can be used as a counterion at up to 2.5 M with essentially no protein contamination and very little nucleotide precipitation. Two successive ethanol precipitations with ammonium chloride can remove all of the unincorporated nucleotides from an in vitro transcription reaction. Removal of all of the supernatant is important for the cleanest results. Remember that ethanol precipitation will recover both your RNA probe and the DNA template, which you might not want in your hybridiztion.