With good experience of AFM, i am sure that you will be able to image CNTs provided that they are fixed to a surface. The last thing that you want is your CNTs to move around whilst you image ! I did not quite understand - Dispersions of CNTs in Al and therefore cannot give you specific advice on said sample.
Two points to consider :
Surface:
The first point is indeed to have as smooth surface as possible to ensure that the phase signal is not affected by the height signal. This is possible very hard to achieve as any small height features will usually be also recorded in the phase. The second element is to ensure that the surface is smooth enough for you to see the CNTs.
Phase contrast limitation
Phase contrast is enhanced by variation in the adhesion properties of the samples vs substrate that you trying to image. Effectively to ensure that you have a good phase contrast - you would like to probe oscillation (intermittent contact mode imaging) to have a strong phase delay whilst imaging either the substrate or the CNTs. This correlates to how much the probe "adhere" to the sample (either physically, chemically or due to charges variations) in either the sample or substrates.
Finally, Phase contrast is a very sensitive imaging technique but difficult to extract "qunatitative data" from. It produces amazing images but that sometimes remain hard to explain, since the information obtained to generate those image is convolulted with topography and adhesion properties of the samples/substrates.
Only on surface... For seeing inside the bulk material maybe nanotomography methods may help? - Not sure if resolution may be enough.
Once upon the time I checked carbon contamination in diamond using EFM. Maybe C-AFM may show you places of another resistivity on surface? I never try to characterize material as mentioned, but if I were You - I would try these methods first.
Of-course AFM provide dispersion of CNTs in Al. More information like depth profile and how the CNTs disperse inside or the surface of the Al can be measure by Time of Flight Secondary Ion Mass Spectrography (ToF-SIMS). Even by changing the phase you can identify and analyze the property of dispersion (Image profile).