Nitin
You're dealing with multiple considerations and multiple issues in this setup.
First, it's a matter of link distribution. When you link to x pages from page 1, this informs search engines "we think these are important destination pages". If you change those links every day, or on every refresh, and if crawlers also encounter those changes, it's going to strain that communication.
This is something that happens naturally on news sites - news changes on a regular basis. So it's not completely invalid and alien to search algorithms to see or deal with. And thus it's not likely their systems would consider this black hat.
The scale and frequency of the changes is more of a concern because of that constantly changing link value distribution issue.
Either X cities are really "top" cities, or they are not.
Next, that link value distribution is further weakened by the volume of links. 25 links per section, three sections - that's 75 links. Added to the links at the top of the page, the "scrolling" links in the main content area of the home page, and the actual "footer" links (black background) so it dilutes link equity even further. (Think "going too thin" with too many links).
On category pages it's "only" 50 links in two sub-footer sections. Yet the total number of links even on a category page is a concern.
And on category pages, all those links dilute the primary focus of any main category page. If a category page is "Cell Phone Accessories in Bangalore", then all of those links in the "Top Cities" section dilute the location. All the links in the "Trending Searches" section dilute the non-geo focus.
What we end up with here then is an attempt to "link to all the things". This is never a best practice strategy.
Best practice strategies require a refined experience across the board. Consistency of signals, combined with not over-straining link equity distribution, and combined with refined, non-diluted topical focus are the best path to the most success long-term.
So in the example of where I said initially that news sites change the actual links shown when new news comes along, the best news sites do that while not constantly changing the primary categories featured, and where the overwhelming majority of links on a single category page are not diluted with lots of links to other categories. Consistency is critical.
SO - where any one or a handful of these issues might themselves not be a critical flaw scale big problem, the cumulative negative impact just harms the site's ability to communicate a quality consistent message.
The combined problem here then needs to be recognized as exponentially more problematic because of the scale of what you are doing across the entire site.