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I want to check license number to make some functional options available. I have found that it is possible to get license data outside of 1c, but I really want to do it without some additional software. Is it possible? Or do I need to make different versions of additional utilities for every version of platform (web, windows, linux)?

The better way is to separate your product into several. You might also add your own licensing, for example checking it through the Internet in the hidden script.
To hide it in Designer mode go to Menu -> Configuration -> Distribute Configuration -> Distribution Options where you can protect your script from viewing and changing by users: Edit -> Include source texts of object modules to distribution.

But to do this I need to have access to installation Id. If I do not have this access I need to add one more license key which I think will be to much for the user.

Other related question. How to separate rapidly application into different distributions? For example no include some subsystems to distribution. I know that there is possibility to separate configuration into different XML-files. But could I use the same method to rapidly make configuration with some script from XML-files? Including just the subsystems I want. It should be really easy to do, otherwise we will struggle making different distributions for every update.

For now you can write a helper application for 1C:Enterprise platform 8.3, which will remove some lines from Configuration.xml and, if necessary, remove some lines from other files which in case of modules you can mark with comments.

And do you have some idea how to get license id? I have some additional services and want to make them available during some period after purchase. But I have to use an additional serial number to make them available for user, because I can not get the id from license.

You can provide your own additional license key to your bonus functionality as a present and ask for activation. I think, that if you limit it with time, some customers might want to enhance the period. In that case the license information will not be enough.

Could I write add-in to 1c (I know that is possible to make built-in components in c) to get license data? Or maybe you have some plugin available? I really need this license number to not make another version of checking hardware parameters.

Yes, you can use Creating external components manual.