Getting an academic position right after an industrial based PhD program I am about to end PhD within next 5-6 months. The PhD program I am enrolled in is different compare to normal universities PhD programs. During first 2 years I took course work from a regular university as an exchange student and afterword I start working in a research institutes whose prime target is to develop projects for the local and international industries.  Luckily or unluckily I am in the section where we deal with various small scale projects; during my 2.5 years of stay I worked on 6 different projects. These projects address totally different issues and topics are independent to each other. Therefore I didn’t get chance to focus on a single topic which can be my PhD thesis. 
As a first author I have published 5 SCI articles including two in top notch journals but all of the articles are not related to each other. In the given situation I am unable to write a good dissertation. I have just 4 months left to fine tune my thesis. After PhD I want to get an academics position but I am bit worrying about my profile.


Is it something positive to have the articles published in different
areas which have no link to each other? 
How much PhD thesis is important for evaluation process? 
As I was working closely with the researchers who mostly focus on standardization and patent activities, none of them has a single SCI publication after graduation even my supervisor had 2 publications around 15 years ago. I am worrying whether the recommendation letter of my supervisor and team leader will be acceptable and effective for the academic position?
Actually, this is a question for your university, you are enrolled to. If they offer "industrial" PhD program, they should explain the criteria for "good" PhD thesis. It is entirely possible that 5 SCI papers are plenty, given the orientation of the program.

If, on the other hand, you are worried about your future career after PhD, yes, there is reason for concern. You enrolled in a program that fits people who want to get employment in the industry, not in the academia. In my opinion it is not the question of what your CV or PhD thesis says, the question is whether you learned enough of the basic research stuff you will need as an academic scientist (as opposed to the industrial developer).

If I would be faced with a candidate like you, I would be very interested in the content of those 5 SCI papers and would like to know which parts of the research were exactly your responsibility. If you implemented a solution, but someone other did rigorous experimental evaluation on all papers, then I would consider you less qualified than someone who did the experimental evaluation part as well (which is usually the case with first authors on journal papers, written in academia).

The unrelated subjects on the other hand would not be a disadvantage.