Is it OK to mix Colony Wars and Frontiers for a 2 player game? Would there be any balance issues?
One main worry is that the trade row might just have high value cards for a while and you are just sitting there buying explorers for a long time
"Balance" typically refers to each player's relative chances of winning. There isn't any inerrant balance changes from the expansions because the trade row is shared between the two players. Even if the trade-row gets full of high-value cards, the game does not favor one player over the other. Unaffordable trade rows happen even with just the base game (I've seen it happen), and Explorers exist for this very reason.
Balance issues aside, all of the Star Realms expansions have a spread of card costs. I do not believe any of them significantly increase the chance of an un-affordable starting trade row.
If you are worried about the trade row being too expensive, by far the most important factor will be the average cost of the cards in the deck. From the card gallery, you can calculate that the average costs in the three large sets are
Core Set: 3.6
Colony Wars: 3.525
Frontiers: 3.4
Thus both the expansions have less expensive cards than Core Set; mixing them together will still result in a less expensive deck.
Technically having a bigger deck does increase the variance of costs you may see. As an extreme example, if you played with a 5 card deck of costs 1,2,3,4,5, then you would always see all 5 costs on the trade row at the start of the game, whereas if you played with lots of copies of that same deck shuffled together, then you would occasionally see starting trade rows of all 1s or all 5s, even though the average value hasn't changed. However, while I haven't crunched the numbers, my guess is that at the scales we are talking about (80-card sets), this effect is not significant compared to the averages discussed above.
There are other things you could also analyze, like
Applying these to the real game is left as an exercise for the reader.