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I am wondering is there some proper terminology which is used to say that deleterious recessive alleles might be able to hide, reducing the the efficacy of selection, in diploid organisms/chromosomes.

I was thinking about Y chromosome linked mutation and their inability to hide from purging by selection behind other alleles by being recessive... perhaps something like recessive sheltering? e.g. "In the Y chromosome mutations are more easily purged because recessive sheltering does not occur" ?

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    $\begingroup$ I don't think you require a special term. In this context recessive implicitly connotes hidden, as in the genotype is hidden because the phenotype is masked (a.k.a. known as wild-type). $\endgroup$ – mdperry May 13 '15 at 10:42
  • $\begingroup$ I think "penetrance" (en.wikipedia.org/wiki/Penetrance) might be the term you're seeking $\endgroup$ – Cantona's Collar May 13 '15 at 11:57
  • $\begingroup$ No, penetrance is the fraction of homozygous mutants that display the loss of function phenotype--for recessive alleles. $\endgroup$ – mdperry May 13 '15 at 12:15
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I think recessive refuge is the term you are looking for (this is the best link I could find, sorry: https://quizlet.com/4176029/bio-experiment-1-and-2-flash-cards/)

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Masked allele is a term that is sometimes used for recessive alleles, and it should be suitable to the situation you describe. A common phrasing could be; "The wild type allele is masking the expression of the deleterious allele X.".

For your particular example you could use:

Deleterious mutations on the Y chromosome are more easily purged since they cannot be masked by alleles on a homologous chromosome.

An example can also be found in the abstract to Otto & Goldstein (1992):

With two copies of every gene, a diploid organism is able to mask recessive deleterious mutations. In this paper we present the analysis of a two-locus model designed to determine when the masking of deleterious alleles favors the evolution of a dominant diploid phase in organisms that alternate between haploid and diploid phases ("alternation of generations").

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