For discussion, I choose to discus on the vitamin B6 (in the pyridoxine form) for comparing hydrochloride salts in medications. Vitamin B6 is most often sold as pyridoxine HCl form. 

At a glance, my assumptions on the hydrochloride form of vitamin B6 are a guess. With vitamin B6, Hydrochloride is typically used to make drugs hardier to temperature, absorption higher in the digestive system and last, less bitter. This must be true with Vitamin B6 in HCL form. 

After further investigation, the vitamin B6 is a group of three substances. Pyridoxine, Pyridoxal and Pyridoxamine. *4

The properties of vitamin B6 differ on the form. The following chart shows the differences of the general properties of pyridoxine and Pyridoxine HCL. The following information was obtained from pubchem.ncbi.nim.nih.gov, see *sources. 

Properties forPyridoxine Pyridoxine Hydrochloride
Molecular Formula*1C8H11NO3 *3C8H12ClNO3
Melting Point*1159-162 °C *3214-215 °C
Appearance*1crystalline solid, White powder*3white crystals or powder 
Stability*1Stable. Incompatible with strong oxidizing agents.*3Stable. Protect from air and light.

There are not available information and I do not have enough knowledge to make rational judgement whether Pyridoxine or Pyridoxine HCL has better affects. However, one would suggest with the information above that Pyridoxine is more stable in temperature and stable in general. Yet on the other hand, Pyridoxine is less stable and has a lower melting temperature. 


All information can be found here (including contributors/additional sources):

*Sources 

*1 http://www.chemspider.com/Chemical-Structure.1025.html?rid=e014d03e-3063-4812-987f-aa7ba21eda19

ChemSpider ID: 1025

*3 http://www.chemspider.com/Chemical-Structure.5797.html?rid=0a526737-eae1-4487-aba3-4cc9bd70bf46&page_num=0

ChemSpider ID: 5797

*4 http://bcpw.bg.pw.edu.pl/Content/3747/researcg_1949_s507.pdf