Why are some housekeeping genes considered better?
Yes, it does matter. Gene expression varies a lot thoughout tissues and living conditions, so you need to test a variety of genes and choose the ones with the smallest variation in the expression between sample and control. 

If you don't find any, you have to test other genes for this purpose. This is important, as this can severly affect the outcome of your experiment, since you normalize to the housekeeping genes. If these are not constant, it will cause problems. Have a look into the references, this helped me a lot.

References:


Accurate normalization of real-time quantitative RT-PCR data by
geometric averaging of multiple internal control genes.
The normalization of gene expression data in melanoma: investigating
the use of glyceraldehyde 3-phosphate dehydrogenase and 18S
ribosomal RNA as internal reference genes for quantitative real-time
PCR.
Normalization of qRT-PCR data: the necessity of adopting a
systematic, experimental conditions-specific, validation of
references.