As outlined here (read it, a lot of background), EVE isn’t just a game of features and mechanisms providing boundaries and pathways for behaviour. EVE functions because features and mechanisms followed behaviour for such a long time that CCP at one point acknowledged that EVE wasn’t a game, but something they called an emergent dynamic. Rightly so, considering all the third parties who use EVE as a petri dish of behavioural studies in sociology, psychology, economics, memetics and other (applied and theoretical) sciences.
So yes, bots are not healthy for the foundation elements of both EVE the game and EVE as life. Keep in mind however that Tranquility is starting to show signs of a tech evolution / transfer in regards to automation in general. There is the traditional botting as players know it, with the tiers of individual and organised botting. But there is also the scripting as we know it from Serenity. With the same tiers. So there’s botrunners, easily identified by CCP, depending on resource allocation for Team Security. And there’s scriptrunners, immensely more difficult to identify.
The introduction of F2P and Alpha’s is more or less intertwined with scriptrunners. Different stimuli, different triggers, but above all the introduction of new types of players with different expectations and patterns in regards to already established gameplay.
So yes, Alpha’s have impact on several levels. More bots, more scriptrunners, more widespread EULA violations of concurrent Alpha’s (and/or Omega combinations). But not because they are Alpha’s as such.
Personally I use the show info → report method as applicable, consistantly, even though it’s never yielded any measurable result. Corp / team members do the same. But we also hook up from time to time to do spring cleaning, like using suicide tactics on the myriads of courier agent bots, or pilots being stupid enough to be open on running scripts.
Where we encounter large style organised forms of either botting, script running or RMT, we put reports together and send those off to security@ccpgames.com, as outlined in earlier devblogs by CCP. Unfortunately only very little of this can be seen to end up in Doomheim or more appropriately worse. More often than not, we can see clear historic progression of reported characters. For example from courier agent runner to Gila/VNI runner to ISK farmer in pubbie alliances after the fake buildup of character identity and (more often than not) fake character sales (most of which do not go over the Character Bazaar).
But let’s put one thing clear. CCP are not complicit in their use. They recognise the fundamental risks of automation applied to the foundation element of economies of scale and perception problems being the number one cause of slipping in retention/acquisition.
CCP’s prime focus is and remains on RMT. I think that should be clear to everyone. It costs them, it hurts their venture and their game.
CCP’s secondary focus is on botting. But the introduction of F2P has created an influx of different behaviour and expectation patterns than what EVE and CCP were used to. Logically, CCP aims to maintain and grow EVE as well as the venture, they have had to make difficult decisions in relation to that. For example relaxing sanction rules in relation to botting as part of making allowances for a wider and more diverse learning curve of new arrivals. We can have an opinion about that, but as we do not know (CCP is not telling, unlike in the past) the results of this, such opinions are irrelevant unless they give rise to a negative perception problem at which point CCP will have to engage on that challenge.
CCP sofar does not appear to distinguish between botrunners and scriptrunners. In industry communications they, unlike other publishers or game developers, make no mention of trends, nor do they seem to distinguish between them for either policies or detection solutions. Unlike for example Blizzard, for whom the rise of scriptrunners using cloud gaming became such an upward curve that they decided to simply ban cloud gaming to close that door. Whether that is smart, or something else, I don’t know. Who cares about fantasy games which - unlike EVE - are not real 
CCP seems, but I could be wrong obviously, to focus primarily on individual activity in all this. Only very rarely do they touch on organised variants, which are far more prevalent and cause far wider ripple effects. When they do it appears to originate more in their focus against RMT than from their anti-botting focus. Like when Roman Abramovich’s cousin was dicking around once upon a time with a certain group of in game alliances in the south east of New Eden. Or when external developments encroach on existing policies and/or presence of RMT elements, like with the drivers of the Casino War once upon a time.
Recently null did its cyclic tour of letting drama between organised runners play out as the scapegoat that distracts from the gentleman’s agreements on organised botting that exist out there. CCP missed it, went quiet on it, clouding matters with lack of clarity and contributing to the growth of existing perception problems.
CCP also has a bit of an issue in regards to exactly that risk of perception problems consolidating here. The focus on individual over organised botting, the seemingly absent monitoring or policies on scriptrunners, the relaxation of sanctions and rules - in combination with lackluster communications and (in spite of intentions) a devblog which really should have gone deeper, as it demonstrated exactly the kind of issues present in player perception in relation to the patterns and trends. Not helpful, unfortunately.
What also doesn’t help is that CCP doesn’t appear to allocate much resources to Team Security in relation to player perception and the cyclic nature of monitoring and actions against botting. I don’t doubt, in spite of personal experiences, that CCP regularly do cleanups, but within the constraints of CCP’s own insights, priorities and available information. See the botrunner/scriptrunner distinction and consider how that presents a massive challenge that largely falls outside of the scope as CCP has outlined it to be to players.
But all this is not the same as being complicit. That stipulates active involvement, with clear knowledge, even policy. CCP is not TianCity, where employees were given carte blanche to make a buck on the side with their own automated accounts and out-of-game sales of items, even services, for the entire time of the waiting period until the agreement to part ways came into effect. And let’s be honest, prior to that Serenity had its TianCity specific issues in these matters.
CCP cares. It’s their venture, their game, and for many it still is their baby.