Well, there are a number of problems. First, the discovery of noncoding RNAs is relatively new and they are difficult to detect, so their number is unknown. In addition, it is unknown how many of them are functional. This has also made it very difficult to define what a gene is and thus made it difficult to count how many genes there are.
Protein coding genes, however, are much easier to deal with, and if you like you can enter any public protein database (at NCBI, for example) and easily query the number of distinct proteins.
Finally, the last problem is that with an organism like human, experimental methods are generally limited by sensitivity (might not detect proteins/RNA at very low concentrations) and the fact that you can't measure all possible cell types/conditions (many gene products will be cell type/condition specific).
Who said life is easy? Somehow things are always complicated in biology...
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