I replaced all the ducts but the trunks in my 1969 home when I replaced the horizontal furnace under the house with a gas pack. I got advice from a friend who was an HVAC contractor. I was surprised to find the trunks and other ducts very clean. I replaced the individual runs with flex primarily for the insulation. I wrapped the trunks with insulation also.
Most organizations concerned with duct cleaning, including EPA, NADCA, NAIMA and the Sheet Metal and Air Conditioning Contractors' National Association (SMACNA) do not currently recommend the routine use of sealants to encapsulate contaminants in any type of duct. Instances when the use of sealants to encapsulate the duct surfaces may be appropriate include the repair of damaged fiber glass insulation or when combating fire damage within ducts. Sealants should never be used on wet duct liner, to cover actively growing mold, or to cover debris in the ducts, and should only be applied after cleaning according to NADCA or other appropriate guidelines or standards.
You should be aware that although a substance may look like mold, a positive determination of whether it is mold or not can be made only by an expert and may require laboratory analysis for final confirmation. For about $50, some microbiology laboratories can tell you whether a sample sent to them on a clear strip of sticky household tape is mold or simply a substance that resembles it.