I'm not entirely sure that I understand the situation, but what concerns me is the comment,
Since it was nicely captured already, the idea of conducting a risk assessment. . trying to predict what could go wrong because of the current storage condition, was conveniently nixed, with a key argument being there is no need to identify the risks and capture on the risk log since we already have documented this on the issue log.
That sets off alarms for me. I don't think that any changes you make to tools will make a difference until there is an integrated, strategic committment to change management. Risks, issues, actions, work packages, etc, all result in changes. Every change should be assessed. Optimize your change control process so that the involved stakeholders have the skill & knowledge to quickly spot implications, and to know when they can be silent.