Ok, so after reading more and re-reading some of the posts, I think I have a grasp on what's going on here, although I could be wrong. It seems to me as though the style of play your group has settled on for Call of Cthulhu is more in keeping with the attitude and principles behind Trail than Call, and in fact that you're already ahead of even Trail in terms of liberally giving away the clues; it sounds like you include even supplementary clues as a standard part of the descriptions of objects and events, unlike Trail. I'm not saying this to disparage Call in any way, nor am I trying to deny the reality that plenty of people adapt Call to get around problems inflicted by failed rolls and so on - I'm just saying that the rules as written of Call are less inclined to give away clues in the vast majority of cases than those of Trail, and you are getting around this by not asking for rolls, something that Trail incorporated into its rules as written for the same reason.
Regarding players missing implications - if they're stuck, you could prompt them on the basis of point spends, or you could simply prompt them without point spends on the basis of their overall ratings. Either of these is simply a diceless mechanic with no chance of failure that achieves the same result that a successful dice roll would in Call, which you have already said is how you handle players getting stuck when playing by those rules.
Regarding point spends - this can be done in different ways, whether by deducting points automatically and offering the advantages (at least when they look stuck, in the case of insight-offering rather than clue-gathering), or asking players if they want to spend, or simply hint that there may be more benefits to be acquired through the use of point spends (e.g. you might say "As a scientist, you feel it's about time you chemically analysed the sample taken from the meteor" or "You have a nagging feeling that you should have dusted for prints more thoroughly" etc).
Point spends, however conducted, should never be seen as a punishment rather than a mechanical support. It's important to remember that losing points is not the same as losing rating levels, and that those points come back eventually. It's also important to remember they are there to be spent - that is their purpose, so spending them is hardly a disadvantage. If anything, failing to adequately spend is the disadvantage, so spending them appropriately is helpful rather than punitive. Finally, bear in mind that most of these spends will come from purely investigative abilities - if these points weren't spent on gathering clues or getting insight into things then they could only possibly be used to gain miscellaneous advantages and shortcuts. Clearly it's better to put the next piece of the puzzle in place than it is to skip over some non-crucial part or do something with fewer resources than usual or whatever.
I think the feeling that it's a punishment comes from comparing it to games in which points equate to your rating, rather than forming a separate pool, or in which points can be liberally spent on other advantages or are needed for other purposes. This is rarely, if ever, the case in Trail. The only time this might concern you is when you're asking for spends from abilities that are general abilities with investigative applications (like Explosives), in which case you are actually depriving the player of a few bonus points to future die rolls. Overall though, it still makes sense to see this as helpful rather than punitive (at least, if we assume the player needs or wants the benefit gained from the spend more than they want a small bonus to a future roll). And frankly, you already seem to give out clues more liberally than Trail intends, so I wouldn't worry too much about using spends to afford insight into the clues already gathered when necessary, since your players may have more points spare on average than other groups anyway.