In the case of most automation tools used for genuine and useful purposes, you do want these to scan your site. These tools wouldn’t be able to do their job if they couldn’t scan your site.
As for their impact, Google knows that PPC reporting tools don’t represent valid clicks on your ads, so these are not counted. In short, you do not need to block ‘good bots’, such as those used by MOZ or SpyFu.
However, there are also plenty of black hat SEO and PPC tools out there which go beyond mere scans and data collecting. Content scraping and link injections are some common methods of.
So although Google may pick up the well-known automation tools, there is a case to be made for monitoring your traffic to watch for black hat tools.