If you're following RFC 4122, v4 and v5 UUIDs can be differentiated by looking at the version number field. (See section 4.1.3 of RFC4122.) So if you're worried about collisions between the two versions, as long as you're marking your UUIDs with the appropriate version, this shouldn't be an issue.
For name-based or "truly random" UUIDs, you don't actually use a clock. That's only for Version 1 UUIDs. (more info in section 4.3 of RFC4122.) They unfortunately kept the names "timestamp" and "clock sequence" for both v4 & v5 UUIDs, even though there is no time-based information in them. Section 4.3 of RFC4122 describes how bytes (octets) from the name-based hash function are placed in the timestamp and clock sequence fields (for v3 & v5 UUIDs) and Section 4.4 describes how random bits are placed in the various UUID fields.
In short, you don't need to know the time to generate a v4 or v5 UUID. Having your servers synchronize their clocks is a good idea generally though; it helps make sense of log files and some protocols freak out if there's too much clock skew.
Using Version 4 UUIDs will require you to have a "truly random" number generator (or something close to it.) I wrote a node.js package for generating UUIDs and made sure it gave the user the option of using /dev/random or /dev/urandom or some other option (pretty sure I defaulted to /dev/random.) At the very least you should know the difference between /dev/random, /dev/urandom and /dev/arandom. I have used /dev/urandom as a random number source, but they were only consumed by local processes (i.e. - i didn't give them out to external clients.) So if we learned later there was a flaw in /dev/urandom, the effects would not be exploitable by external actors.
If you're dealing with financial or PII data, there may be regulatory requirements on random number generation. Heaven help you if you're recording credit card numbers in there somewhere.
It's probably hard to get detailed advice without knowing the content of the data being stored and the context of it's use. But you can plan for the worst by:
a. using UUID generation software that allows you to securely specify a specific source for your (pseudo) random numbers.
b. understand that a UUID generator might block for an indeterminate amount of time if you're forced to use a PRNG that waits to collect sufficient entropy.
c. here's my old UUID generating code. i don't recommend using it; it's just too old. but it does give an example of using an interface that lets you select the source of random numbers. it also probably doesn't work on windows: https://github.com/OhMeadhbh/node-mug