There are different points of view about using system 'tune-up' or tweaking software, of which System Mechanic is just one example. I've come around to believe that the point of view of 'if it isn't broken, don't fix it' is the safest approach in terms of preserving a system's safety and security. There are many tweaking programs that promise to speed up, clean up, or otherwise improve and maintain system performance on a computer. They generally try to do that by changing OS internal settings in the registry, removing certain programs from drives, and so on. In so doing, they have very powerful influence over how the system may operate, and they can cause major problems if they or the user have made even one poor choice in whatever is being altered or removed.
Often, bad results only show up later when some function seems to 'break' or starts to fail. Moreover, I've found that the use of generalized tweaking tools tend to cause a cumulative increase in fragility of an OS over time. As the changes made by the tool accumulate, the system tends to become less and less robust in its ability to withstand other issues that might and do arise. For example, when item A is tweaked to achieve something, item B must also often be tweaked to compensate for the side-effects of the item A adjustment. At some point, enough settings become perturbed that the system is rendered less stable or sufficiently non-standard that things eventually start to break, often in surprising ways. Because all this goes on in the bowels of the OS, it's usually invisible until something unpleasant suddenly starts happening. Because the changes made by the tweaking tool are invisible, all too often, reinstalling the OS is the only way out of the maze of compounded tweaks that have finally let to a major system problem.
As @leocg notes, system hardware (especially drives or RAM) can also begin failing, and normal wear and tear on an OS and its software modules (OS updates, power-fails with files open, etc) can create problems similar to what you experienced. However, I would personally think long and hard about whether or not to re-apply a tweaking tool like System Mechanic and whether any of its performance gains you've actually experienced in the past are worth the added risks to system stability.
By the way, safe mode is simply the OS loading itself without external drivers and with bare-bones default settings. If it's causing problems, it indicates the OS files themselves are messed up. That can be the result of either hardware problems, corrupted OS files, or an over-aggressive tweaking tool that's finally fouled things up.