The original purpose of standardized tests was to provide a means to make sure that all students had an opportunity to learn the same minimum content. It is a great shame that they have been misused and misapplied.
Another misconception concerning standardized tests is that they are all on bubble sheets - the NAEP tests contain both questions (some m/c, some essay) as well as hands-on performance-based problems - just what you are preparing your students for!
That said, just because you teach hands-on, it does not mean you should not prepare your students for standardized (bubble) tests, because, like it or not, they will be taking them for science at some point in their academic careers. In my state, they have to pass a standardized test in biology to graduate and some of your students may, at some point, take an advanced placement test. Multiple choice and short or long answer essay questions can be written that address higher order thinking skills, it just takes some care and practice.
And some are already available to you online. If you do a search in the Learning Center for NAEP there are links to 16 webseminars that provide both interpretation of NAEP test results AND links to sample questions that have already been used and validated at various grade levels. There are also links to the website where additional questions can be found. Perhaps, instead of giving tests, you could incorporate these questions into entry/exit questions or class reviews over topics - that way you could be preparing your students to answer standardized test-style questions without sacrificing your class time to long drawn-out tests. And the results could be useful to you for diagnostic or formative purposes, as well.
If you have time to take a course in designing assessment, it is a worthwhile use of time. If not, there are a number of good introductory materials here in the Learning Center. Hands-on inquiry teaching is good but using a variety of assessment tools makes sure we don't miss recognizing student alternative conceptions.